RE: [gmx-users] g_rdf -surf
Hello, I am trying to calculate the RDF of water next to surface of certain residues. I used the an index file which includes the residues as the first group, and the #12 option (SOL) in the g_rdf, and used the option '-surf res' on the prompt. However, the calculated RDF rises up to 41000 in long distances. It appears that it is normalized (as specified by the help). How can I normalize this function? Best, Paymon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_rdf -surf
Hello, Thanks for your attention. A word was missing in my previous e-mail!! The g(r) is NOT normalized. Here was my command: g_rdf -f traj.xtc -s topol.tpr -n reidues_atoms.ndx -o gofr -surf res The index file includes atoms in the side chain exposed to the solvent: [ SideChain_&_r_13_r_17_r_19-21_r_24 ] 144 145 146 147 148 149 150 151 152 189 190 191 192 193 194 195 196 197 198 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 285 286 287 288 289 290 291 292 293 294 295 296 297 298 So, I am trying to calculate the RDF of water molecules (SOL) with respect to the surface of the residues whose side chain atoms are listed in the index file. What I get is a small peak in the order of 0.05 the beginning, and then, g(r) is increasing to 41000. Sorry for inconveniences in the first iteration. Best, paymon From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: February-13-12 12:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf -surf On 13/02/2012 5:54 PM, Payman Pirzadeh wrote: Hello, I am trying to calculate the RDF of water next to surface of certain residues. I used the an index file which includes the residues as the first group, and the #12 option (SOL) in the g_rdf, and used the option '-surf res' on the prompt. Please supply the actual command line copied and pasted, as well as which groups you specified and what they contain. The information above is confusing. However, the calculated RDF rises up to 41000 in long distances. It appears that it is normalized (as specified by the help). How can I normalize this function? If it's already normalized, what do you want to do? 41000 is what quantity? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_rdf -surf
By the way, The g(r) = 0.05 is around 1.75 A, which sounds to be consistent with literature, but as r increases towards 10A, instead of converging to a value of 1, g(r) goes towards 41000. I want to return the value of g(r) to 1. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: February-13-12 12:24 AM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] g_rdf -surf Hello, Thanks for your attention. A word was missing in my previous e-mail!! The g(r) is NOT normalized. Here was my command: g_rdf -f traj.xtc -s topol.tpr -n reidues_atoms.ndx -o gofr -surf res The index file includes atoms in the side chain exposed to the solvent: [ SideChain_&_r_13_r_17_r_19-21_r_24 ] 144 145 146 147 148 149 150 151 152 189 190 191 192 193 194 195 196 197 198 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 285 286 287 288 289 290 291 292 293 294 295 296 297 298 So, I am trying to calculate the RDF of water molecules (SOL) with respect to the surface of the residues whose side chain atoms are listed in the index file. What I get is a small peak in the order of 0.05 the beginning, and then, g(r) is increasing to 41000. Sorry for inconveniences in the first iteration. Best, paymon From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: February-13-12 12:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf -surf On 13/02/2012 5:54 PM, Payman Pirzadeh wrote: Hello, I am trying to calculate the RDF of water next to surface of certain residues. I used the an index file which includes the residues as the first group, and the #12 option (SOL) in the g_rdf, and used the option '-surf res' on the prompt. Please supply the actual command line copied and pasted, as well as which groups you specified and what they contain. The information above is confusing. However, the calculated RDF rises up to 41000 in long distances. It appears that it is normalized (as specified by the help). How can I normalize this function? If it's already normalized, what do you want to do? 41000 is what quantity? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_energy
Hello, I am using gromacs 4.5.4. In g_energy I see an option about #surf*surfTen. Could you please clarify how it is calculated? In a system with a protein and water, what does it correspond to? Best, Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: March-29-12 7:23 PM To: Acoot Brett; Discussion list for GROMACS users Subject: Re: [gmx-users] protein melting experiment by GROMACS Acoot Brett wrote: > Dear All, > > I remember before I have read a something on melting the protein from > a predefined starting temperature to a predefined end temperature by > MD, so that after the MD we can look at the whole process to see which > part of the protein unfold earlier, which part of the protein of the > protein unfold earlier. No I cannot find that introduction. > > After we equilibriate the protein system, will you please tell me how > to define the temperature gradient from the start temperature to the > end temperature in the mdp file? Or do you have a protocol on it? > See the manual regarding simulated annealing. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_energy surf*surftens
Hello, In calculation of the surf*surftension with g_energy, does this quantity have any meaning when one deals with a protein in water(water fills up the box)? Can it be indicative of the surface tension of protein and water? Thanks. Paymon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] selecting res CYS from G53a5 using pdb2gmx
Hi, I am using gromacs 4.5.4, and I am generating a topology file using G53a5 force field. My protein has a Cys residue which is supposed to be in thiolate state (negatively charged side chain). During issuing the pdb2gmx command I use the switch -inter to be prompted about the charge state of the ionisable side chains, but it asks nothing about Cys side chains except about they being involved in disulfide bonds. My questions are: 1. how can I get pdb2gmx ask me about the charge status of Cys residues? Or do I need to manually change their status in the topology file and output gro file (removing the HG)? 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, the total charge of the residue does not add to -1 but -0.5. Is anyone aware of any modifications to this force field parameters? Best, Payman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
Dear Justin, I have been able to temporarily solve my force field parameter problem (at least test the new parameters). I defined a new Cys residue say CYSA (as anion) in the rtp file. But how can I prevent the pdb2gmx from adding hydrogen to the Cysteine residue? Addition of this extra hydrogen changes all the indexing. Can utilization of an index file during topology generation? or can "grompp -renum" help in this case? I am left wondered how to force pdb2gmx to prompt to ask me for the selection of the type, when several types of a particular residue is defined in the rtp file? Your help is appreciated in advance. Best, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-06-13 6:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/6/13 4:45 PM, Payman Pirzadeh wrote: > Hi, > I am using gromacs 4.5.4, and I am generating a topology file using > G53a5 force field. My protein has a Cys residue which is supposed to > be in thiolate state (negatively charged side chain). During issuing > the pdb2gmx command I use the switch -inter to be prompted about the > charge state of the ionisable side chains, but it asks nothing about > Cys side chains except about they being involved in disulfide bonds. My questions are: > 1. how can I get pdb2gmx ask me about the charge status of Cys > residues? Or do I need to manually change their status in the topology > file and output gro file (removing the HG)? > 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, > the total charge of the residue does not add to -1 but -0.5. Is anyone > aware of any modifications to this force field parameters? I don't know of any. The AMBER force fields have parameters for the thiolate form of cysteine, but I've never seen them for Gromos96 force fields. That doesn't mean they don't exist, of course, but this is the sort of thing one should research prior to choosing a force field and then hoping for a solution later ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
Two clarifications: 1. can utilization of an index file help during topology generation for my problem? 2. I use -inter for getting prompted for LYS, ARG, ... but CYS is not one of them. Cheers, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: January-07-13 5:28 PM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx Dear Justin, I have been able to temporarily solve my force field parameter problem (at least test the new parameters). I defined a new Cys residue say CYSA (as anion) in the rtp file. But how can I prevent the pdb2gmx from adding hydrogen to the Cysteine residue? Addition of this extra hydrogen changes all the indexing. Can utilization of an index file during topology generation? or can "grompp -renum" help in this case? I am left wondered how to force pdb2gmx to prompt to ask me for the selection of the type, when several types of a particular residue is defined in the rtp file? Your help is appreciated in advance. Best, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-06-13 6:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/6/13 4:45 PM, Payman Pirzadeh wrote: > Hi, > I am using gromacs 4.5.4, and I am generating a topology file using > G53a5 force field. My protein has a Cys residue which is supposed to > be in thiolate state (negatively charged side chain). During issuing > the pdb2gmx command I use the switch -inter to be prompted about the > charge state of the ionisable side chains, but it asks nothing about > Cys side chains except about they being involved in disulfide bonds. > My questions are: > 1. how can I get pdb2gmx ask me about the charge status of Cys > residues? Or do I need to manually change their status in the topology > file and output gro file (removing the HG)? > 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, > the total charge of the residue does not add to -1 but -0.5. Is anyone > aware of any modifications to this force field parameters? I don't know of any. The AMBER force fields have parameters for the thiolate form of cysteine, but I've never seen them for Gromos96 force fields. That doesn't mean they don't exist, of course, but this is the sort of thing one should research prior to choosing a force field and then hoping for a solution later ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
Dear Justin, Thanks for your suggestions. It all made sense. But I ran into a strange problem. I checked the mail list, and all I found was about misspelling the force field name. I copied the whole gromos53a5.ff directory into my working folder, copied the modified .rtp, .dat and .hdb files into the gromos53a5.ff folder, and issued: pdb2gmx_d_mpi -f protein.pdb -p protein-CYA.top -o protein-CYA.gro -inter -ff gromos53a5.ff but what I got was: Program pdb2gmx_d_mpi, VERSION 4.5.4 Source code file: pdb2top.c, line: 239 Fatal error: Could not find force field 'gromos53a5.ff' in current directory, install tree or GMXDATA path. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors If I do not add the -ff option, the default pdb2gmx command works, by opening the force field from the default path. I tried 'source GMXRC' from my working folder, but same error pops up. I am not sure what I am missing here?! Sorry for mass of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-07-13 5:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/7/13 7:36 PM, Payman Pirzadeh wrote: > Two clarifications: > 1. can utilization of an index file help during topology generation > for my problem? No. Reading pdb2gmx -h will tell you this. > 2. I use -inter for getting prompted for LYS, ARG, ... but CYS is not > one of them. CYS should be one of the choices. If you want to make your life really easy, name your residue "CYA" instead of "CYSA" so that the selection machinery never deals with it. Make sure you have an appropriate .hdb entry as well and pdb2gmx will do whatever you tell it. -Justin > Cheers, > > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Payman Pirzadeh > Sent: January-07-13 5:28 PM > To: 'Discussion list for GROMACS users' > Subject: RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx > > Dear Justin, > I have been able to temporarily solve my force field parameter problem > (at least test the new parameters). I defined a new Cys residue say > CYSA (as > anion) in the rtp file. But how can I prevent the pdb2gmx from adding > hydrogen to the Cysteine residue? Addition of this extra hydrogen > changes all the indexing. Can utilization of an index file during > topology generation? or can "grompp -renum" help in this case? > I am left wondered how to force pdb2gmx to prompt to ask me for the > selection of the type, when several types of a particular residue is > defined in the rtp file? > Your help is appreciated in advance. > Best, > > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin Lemkul > Sent: January-06-13 6:54 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx > > > > On 1/6/13 4:45 PM, Payman Pirzadeh wrote: >> Hi, >> I am using gromacs 4.5.4, and I am generating a topology file using >> G53a5 force field. My protein has a Cys residue which is supposed to >> be in thiolate state (negatively charged side chain). During issuing >> the pdb2gmx command I use the switch -inter to be prompted about the >> charge state of the ionisable side chains, but it asks nothing about >> Cys side chains except about they being involved in disulfide bonds. >> My > questions are: >> 1. how can I get pdb2gmx ask me about the charge status of Cys >> residues? Or do I need to manually change their status in the >> topology file and output gro file (removing the HG)? >> 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, >> the total charge of the residue does not add to -1 but -0.5. Is >> anyone aware of any modifications to this force field parameters? > > I don't know of any. The AMBER force fields have parameters for the > thiolate form of cysteine, but I've never seen them for Gromos96 force > fields. That doesn't mean they don't exist, of course, but this is > the sort of thing one should research prior to choosing a force field > and then hoping for a solution later ;) > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/just
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
Dear Justin, Thanks for the tips. Things worked smoothly up to the point when I wanted to run an actual simulation. When I wanted to run grompp for a NVT simulation, I got this error message: Fatal error: 7 atoms are not part of any of the T-Coupling groups I realized that that in my mdp file, I had: Tcoupl = Nose-Hoover tau_t = 0.2 0.2 0.2 tc-grps = Protein SOL CL- ref_t = 310 310 310 I noticed that this warning is related to the CYA residue. So I added CYA as a new group to the above list and problem was solved. But what remains strange/scary to me is that I defined CYA in residuetypes.dat! Shouldn't grompp consider the new residue as part of the protein? Won't this separate temperature coupling of a residue and protein cause strange behavior? Sorry for inconveniences. Best, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 3:55 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 1:37 AM, Payman Pirzadeh wrote: > Dear Justin, > Thanks for your suggestions. It all made sense. > But I ran into a strange problem. I checked the mail list, and all I > found was about misspelling the force field name. I copied the whole > gromos53a5.ff directory into my working folder, copied the modified > .rtp, .dat and .hdb files into the gromos53a5.ff folder, and issued: > pdb2gmx_d_mpi -f protein.pdb -p protein-CYA.top -o protein-CYA.gro > -inter -ff gromos53a5.ff but what I got was: > > Program pdb2gmx_d_mpi, VERSION 4.5.4 > Source code file: pdb2top.c, line: 239 > > Fatal error: > Could not find force field 'gromos53a5.ff' in current directory, > install tree or GMXDATA path. > For more information and tips for troubleshooting, please check the > GROMACS website at http://www.gromacs.org/Documentation/Errors > > If I do not add the -ff option, the default pdb2gmx command works, by > opening the force field from the default path. I tried 'source GMXRC' > from my working folder, but same error pops up. I am not sure what I > am missing here?! You're using the wrong syntax. The option -ff should take just the prefix of the force field directory, i.e. "-ff gromos53a5" which causes pdb2gmx to search for a gromos53a5.ff directory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
These are the lines in my residuetype.dat: CYS Protein CYS1Protein CYS2Protein CYSHProtein CYA Protein DALAProtein Have I missed anything? How can I couple CYA with protein under this conditions? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 4:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 6:09 PM, Payman Pirzadeh wrote: > Dear Justin, > Thanks for the tips. Things worked smoothly up to the point when I > wanted to run an actual simulation. When I wanted to run grompp for a > NVT simulation, I got this error message: > > Fatal error: > 7 atoms are not part of any of the T-Coupling groups > > I realized that that in my mdp file, I had: > > Tcoupl = Nose-Hoover > tau_t = 0.2 0.2 0.2 > tc-grps = Protein SOL CL- > ref_t = 310 310 310 > > I noticed that this warning is related to the CYA residue. So I added > CYA as a new group to the above list and problem was solved. But what > remains strange/scary to me is that I defined CYA in residuetypes.dat! > Shouldn't grompp consider the new residue as part of the protein? > Won't this separate temperature coupling of a residue and protein cause strange behavior? Yes, as does the fact that you're coupling ions separately from the solvent. If you correctly added CYA to residuetypes.dat, this shouldn't happen. Do not couple it separately from the protein; that makes no sense. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
Hi, Found my solution; made an index file which had the protein and CYA in the same group. Thanks for all your helps Justin. P. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 4:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 6:09 PM, Payman Pirzadeh wrote: > Dear Justin, > Thanks for the tips. Things worked smoothly up to the point when I > wanted to run an actual simulation. When I wanted to run grompp for a > NVT simulation, I got this error message: > > Fatal error: > 7 atoms are not part of any of the T-Coupling groups > > I realized that that in my mdp file, I had: > > Tcoupl = Nose-Hoover > tau_t = 0.2 0.2 0.2 > tc-grps = Protein SOL CL- > ref_t = 310 310 310 > > I noticed that this warning is related to the CYA residue. So I added > CYA as a new group to the above list and problem was solved. But what > remains strange/scary to me is that I defined CYA in residuetypes.dat! > Shouldn't grompp consider the new residue as part of the protein? > Won't this separate temperature coupling of a residue and protein cause strange behavior? Yes, as does the fact that you're coupling ions separately from the solvent. If you correctly added CYA to residuetypes.dat, this shouldn't happen. Do not couple it separately from the protein; that makes no sense. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
I had modified three files: aminoacids.rtp, aminoacids.hdb and residuetypes.dat. All these modifications were done prior running pdb2gmx. So, I will be glad if you could let me know what the problem is. Best, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 6:58 PM, Payman Pirzadeh wrote: > Hi, > Found my solution; made an index file which had the protein and CYA in > the same group. > Thanks for all your helps Justin. > I'm glad you found a solution, but for the purpose of being thorough I need to say that this should not be necessary. A residue listed as "Protein" in residuetypes.dat, if added prior to running pdb2gmx, should lead to seamless integration in the topology when running all subsequent steps in preparing the system. It is unclear to me what's going on here. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
Since gromacs is globally installed on the cluster, I am making local modifications. What was strange was I modified the three files, and I ran pdb2gmx with them, and it failed (it could not find certain atoms?!). Then I copied the whole gromos53a5 folder to my working directory and moved these files into it, and I used the -ff option, but it still opened the global folder. So, I kept the three modified files in my working directory + the grooms folder with the modified files, then it worked. The topology contained the new parameters. I guess there might be sth with how pdb2gmx finds the database files. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 5:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 7:25 PM, Payman Pirzadeh wrote: > I had modified three files: aminoacids.rtp, aminoacids.hdb and > residuetypes.dat. All these modifications were done prior running pdb2gmx. > So, I will be glad if you could let me know what the problem is. From that description, everything should be fine. Are you making local modifications (i.e. in the working directory with a copy of the force field) or making modifications in $GMXLIB? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
Dear Justin, You are absolutely right. I only needed to keep the modified 'residuetypes.dat' in my working directory not the .rtp and .hdb files. I retried the whole process and this time CYA was not a separate group. Great experience. Thanks for your patience and help. Best, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 8:05 PM, Payman Pirzadeh wrote: > Since gromacs is globally installed on the cluster, I am making local > modifications. What was strange was I modified the three files, and I > ran pdb2gmx with them, and it failed (it could not find certain > atoms?!). Then I copied the whole gromos53a5 folder to my working > directory and moved these files into it, and I used the -ff option, > but it still opened the global folder. So, I kept the three modified > files in my working directory + the grooms folder with the modified > files, then it worked. The topology contained the new parameters. I > guess there might be sth with how pdb2gmx finds the database files. > The proper approach for making local modifications is to create a complete force field directory with all necessary files within it. The residuetypes.dat file must be in the working directory, not any subdirectory thereof, and you must issue all commands from within that directory. Otherwise, Gromacs programs revert to the copy in $GMXLIB. I suspect any of these factors will explain what you're observing with respect to intermittent successes - you're either moving around directories or putting files in the wrong place(s). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] changing protonation state of a residue during a simulation
Hello, I am simulating a protein using side chain pKa values estimated from PROPKA based on crystal structure of the protein. I re-estimated the pKa of side chains after running 10 independent replica of 50ns (500ns in total) of NPT simulations. It turned out that the average pKa of a surface Glu was overestimated in the crystal structure (protonated), and needs to be reconsidered (not protonated). I was wondering how I can re-assign the protonation state of this single residue without going through pdb2gmx (or may be I have to) to keep the current conformation of the protein and currently equilibrated solvent molecules? Is there a way to continue the current simulations I have and only change the charge of this single surface Glu? Thanks for your help. Payman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_covar -ascii
Hello, I am interested in dynamical analysis of my protein. In the manual, it says -ascii generates a file that includes the whole covariance matrix, and -xpma writes the atomic covariance matrix per pair of atoms. I was wondering if there is a way to have this atomic covariaces in the .dat file with -ascii switch. Otherwise, is there a script in gromacs that converts the xpm to an ascii file? In addition, is the -xpma output normalized? Thanks for your help. Payman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs
Hello, I am trying to generate a topology file for my protein which has three disulfide bonds using ffG53a5. I realized in the topology file that the force field parameters for bonds, angle and dihedrals of my S-S bonds are missing. I found the following thread about this issue: http://lists.gromacs.org/pipermail/gmx-users/2011-November/066371.html Using version 4.5.4, I typed grompp -p topol.top -pp topol-processed.top -f systemem.mdp -c protein-solvated-neutral.gro to generate the processed topology file. These terms are still missing in the processed topology file, but grompp complained nothing. Am I safe? Is there still sth going on that takes care of the missing terms in the topology file? Thanks for your help. Best, Paymon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] restarting a crashed job
Hello, My simulation crashed in the middle and I used the "-cpi checkpoint.cpt -append" option to continue. However, GROMACS cannot continue and complains about not being able to open the corresponding .trr file. I checked my folder, the trr file is there and the name is the same as the *.tpr and *.cpt files. What else could have caused this problem? Thanks. P. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] itp and gro files
I was wondering if the order of sites in .gro file should be the same as in .itp file. Payman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] itp and gro files
Thank you very much. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: May 6, 2009 8:25 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] itp and gro files Payman Pirzadeh wrote: > I was wondering if the order of sites in .gro file should be the same as > in .itp file. > > Yes, otherwise, you will see grompp warnings indicating that atom names in the .top and .gro do not match. -Justin > > Payman > > > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Some molecules disconnected into many parts after EM
Hi Yanmei, I had this problem with water molecules, and I found that any time I changed the constrains without changing the boxes I generated through 'editconf'. So, after changing the constrains, I had to redo all my box generation process, then it was fine. But I ran into another problem and that was I had a separate row of molecules out of my box (which I do not know where they come from)! Payman From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: May 7, 2009 6:06 PM To: gmx-users@gromacs.org Subject: [gmx-users] Some molecules disconnected into many parts after EM Dear users: I set up a 8nm cubic box with 6 long chain molecules. After EM, there is no error message. However I found that in the gro file by visualization, 2 of the chains has been split in many parts, which means many bonds in the molecules disconnected. And also the other 4 are good. I checked em.log and eveyting looks fine. Steepest Descents converged to machine precision in 1545 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.51461594735782e+03 Maximum force = 2.66505909651672e+02 on atom 1256 Norm of force = 9.84300153087768e+00 Anyone knows how to solve the problem? Thanks in advance! -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make install-mdrun
Hi All, I realized that I am missing (Lib and bin folders) analysis tools and mdrun MPI. I re-installed the GROMACS 4.0.3, and I found that when I get to 'make install-mdrun' the following messages show up ( I am just copying last lines): make[2]: *** [install-libLTLIBRARIES] Error 1 make[2]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/mdlib' make[1]: *** [install-am] Error 2 make[1]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/mdlib' (cd ./src/kernel && make install-mdrun ; exit 0) make[1]: Entering directory `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/kernel' /bin/sh ../../config/mkinstalldirs /usr/local/gromacs/bin mkdir -p -- /usr/local/gromacs/bin mkdir: cannot create directory `/usr/local/gromacs': Permission denied make[1]: *** [install-mdrun] Error 1 make[1]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/kernel' I changed the permissions and I am still receiving the same message. I will e appreciated if someone tell me what is going wrong?! Payman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] make install-mdrun
Thanks Diego, But, the latest I found on downloads of gromcs webpage was 4.0.3! Is 4.0.4 somewhere else? Payman From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Diego Enry Gomes Sent: May 8, 2009 11:27 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make install-mdrun get gromacs 4.04 Confirm if you changed the permissions correctly and can write anywhere in /usr/local/ Are you doing this as 'root' or super user (sudo) ? Because if you are just a regular user, will won't be able to change the permissions in /usr/local/. So, configure gmx to be installed in your local dir. ./configure --prefix=/global/home/pirzadeh/gmx404 On May 8, 2009, at 10:10 AM, Payman Pirzadeh wrote: Hi All, I realized that I am missing (Lib and bin folders) analysis tools and mdrun MPI. I re-installed the GROMACS 4.0.3, and I found that when I get to 'make install-mdrun' the following messages show up ( I am just copying last lines): make[2]: *** [install-libLTLIBRARIES] Error 1 make[2]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/mdlib' make[1]: *** [install-am] Error 2 make[1]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/mdlib' (cd ./src/kernel && make install-mdrun ; exit 0) make[1]: Entering directory `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/kernel' /bin/sh ../../config/mkinstalldirs /usr/local/gromacs/bin mkdir -p -- /usr/local/gromacs/bin mkdir: cannot create directory `/usr/local/gromacs': Permission denied make[1]: *** [install-mdrun] Error 1 make[1]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/kernel' I changed the permissions and I am still receiving the same message. I will e appreciated if someone tell me what is going wrong?! Payman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] make install-mdrun
Thanks Justin. I thought by default everything should be in downloads. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: May 8, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make install-mdrun Payman Pirzadeh wrote: > Thanks Diego, > > But, the latest I found on downloads of gromcs webpage was 4.0.3! Is > 4.0.4 somewhere else? The homepage and wiki both have the links to 4.0.4, or you can simply change the ftp link to point to gromacs-4.0.4 instead of 4.0.3. -Justin > > > > Payman > > > > *From:* gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Diego Enry Gomes > *Sent:* May 8, 2009 11:27 AM > *To:* Discussion list for GROMACS users > *Subject:* Re: [gmx-users] make install-mdrun > > > > get gromacs 4.04 > > > > Confirm if you changed the permissions correctly and can write anywhere > in /usr/local/ > > > > Are you doing this as 'root' or super user (sudo) ? Because if you are > just a regular user, will won't be able to change the permissions in > /usr/local/. So, configure gmx to be installed in your local dir. > > > > ./configure --prefix=/global/home/pirzadeh/gmx404 > > > > > > On May 8, 2009, at 10:10 AM, Payman Pirzadeh wrote: > > > > Hi All, > > I realized that I am missing (Lib and bin folders) analysis tools and > mdrun MPI. I re-installed the GROMACS 4.0.3, and I found that when I get > to 'make install-mdrun' the following messages show up ( I am just > copying last lines): > > > > make[2]: *** [install-libLTLIBRARIES] Error 1 > > make[2]: Leaving directory > `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/mdlib' > > make[1]: *** [install-am] Error 2 > > make[1]: Leaving directory > `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/mdlib' > > (cd ./src/kernel && make install-mdrun ; exit 0) > > make[1]: Entering directory > `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/kernel' > > /bin/sh ../../config/mkinstalldirs /usr/local/gromacs/bin > > mkdir -p -- /usr/local/gromacs/bin > > mkdir: cannot create directory `/usr/local/gromacs': Permission denied > > make[1]: *** [install-mdrun] Error 1 > > make[1]: Leaving directory > `/global/home/pirzadeh/GROMACS4.0.3/gromacs/src/kernel' > > > > I changed the permissions and I am still receiving the same message. I > will e appreciated if someone tell me what is going wrong?! > > > > Payman > > ___ > gmx-users mailing listgmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] -np switch
Hello, When we use 'mdrun' or 'grompp' with the switch '-np' we specify the number of nodes according to the manual. Does it mean if the nodes have 2 processors, then the simulation will be run on 4 CPUs or in -np we should specify 4 instead of 2? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs on glacier.westgrid.ca
Hi All, Is there anyone who is running gromacs on glacier.westgrid.ca machine? If yes, I will be appreciated if he/she can tell me how to run gmx on this facility. I either get error messages which says either the executable or the topology file can not be found. Regards, Payman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk, Thanks for your e-mail. The message that cluster sends is: "Running on 4 processors. Starting run at: Sat May 16 17:13:28 PDT 2009 Warning: Command line arguments for program should be given after the program name. Assuming that ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that -s is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that npttest is a command line argument for the program. Missing: program name Program -path either does not exist, is not executable, or is an erroneous argument to mpirun. Job finished at: Sat May 16 17:13:28 PDT 2009" The message that GROMACS has in log file is: "Program mdrun, VERSION 3.3.1 Source code file: gmxfio.c, line: 706 Can not open file: topol.tpr" This is while I have the topology file in the same folder. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar Sent: May 19, 2009 12:25 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca Hi Payman, That is probably not the only grid facility on which Gromacs may be run and it would be helpful if you could give specifications of it (WMS software e.g.), which could give you more response. Also, it would be helpful if you'd be able to give more information regarding the output. Then you'd also have to ask the question whether your problem is grid related or gromacs related. In the former case you'd better consult support from the facility you're trying to use. Cheers, Tsjerk On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh wrote: > Hi All, > > Is there anyone who is running gromacs on glacier.westgrid.ca machine? If > yes, I will be appreciated if he/she can tell me how to run gmx on this > facility. I either get error messages which says either the executable or > the topology file can not be found. > > Regards, > > > > Payman > > > > > > ___ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] gromacs on glacier.westgrid.ca
Hi Justin,
Following is the script I use. But remember several points:
1. I compiled the gmx with double precision and did not rename the code to
mpi. I kept whatever was produced with _d suffix.
2. I use the same script for other codes and they work (I am using other MD
code for special purposes and a QM code as well).
3. This script follows the guidelines of glacier as well. It is available
online at http://www.westgrid.ca/support/quickstart/glacier
#!/bin/bash
#PBS -S /bin/bash
# Torque script for running an MPI program pn on glacier
# 2005-05-26 DSP
# This presumes code compiled with the Intel compiler.
# For example:
# /global/software/mpich-1.2.5.2/ssh/bin/mpif90 pn.f -o pn
#PBS -N sixsite-test
#PBS -l walltime=240:00:00
#PBS -l nodes=2:ppn=2
#PBS -l qos=parallel
MPIRUN="/global/software/mpich-1.2.5.2/ssh/bin/mpirun"
cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"
echo "Node file: $PBS_NODEFILE :"
echo "-"
cat $PBS_NODEFILE
echo "-"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
echo "Starting run at: `date`"
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
echo "Job finished at: `date`"
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: May 19, 2009 12:36 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
"Running on 4 processors.
Starting run at: Sat May 16 17:13:28 PDT 2009
Warning: Command line arguments for program should be given
after the program name. Assuming that
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that -s is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that npttest is a
command line argument for the program.
Missing: program name
Program -path either does not exist, is not
executable, or is an erroneous argument to mpirun.
Job finished at: Sat May 16 17:13:28 PDT 2009"
The message that GROMACS has in log file is:
"Program mdrun, VERSION 3.3.1
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr"
This is while I have the topology file in the same folder.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Tsjerk Wassenaar
Sent: May 19, 2009 12:25 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful if you'd be able to give more information regarding
the output. Then you'd also have to ask the question whether your
problem is grid related or gromacs related. In the former case you'd
better consult support from the facility you're trying to use.
Cheers,
Tsjerk
On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh
wrote:
> Hi All,
>
> Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
> yes, I will be appreciated if he/she can tell me how to run gmx on this
> facility. I either get error messages which says either the executable or
> the topology file can not be found.
>
> Regards,
>
>
>
> Payman
>
>
>
>
>
> ___
> gmx-users mailing list gmx-us...@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
__
RE: [gmx-users] gromacs on glacier.westgrid.ca
Hi Nicolas,
Thanks for the tips!
Yes, that's what I thought yesterday. Main problem is I think there is an
older version of GROMACS installed on Glacier and if I do not source the
path, it will take the cluster one not mine. I passed that phase. Now I am
checking if I can run the job in parallel with no problems.
Are you in UofC?
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Nicolas Sapay
Sent: May 20, 2009 2:26 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
Hello Payman,
Westgrid (and Glacier) has several pages of doc on its website about running
Gromacs and compiling softwares. I used to run (my own compilation of)
Gromacs on Glacier and never had any particular problem.
You just have to make sure you compile it with the correct mpicc and fftw
libraries. You also have make sure that you source the appropriate path to
mdrun in your script and that your GMXLIB path is correctly set.
Hope that helps,
Nicolas
Payman Pirzadeh a écrit :
> Hi Justin,
> Following is the script I use. But remember several points:
> 1. I compiled the gmx with double precision and did not rename the
> code to mpi. I kept whatever was produced with _d suffix.
> 2. I use the same script for other codes and they work (I am using
> other MD code for special purposes and a QM code as well).
> 3. This script follows the guidelines of glacier as well. It is
> available online at http://www.westgrid.ca/support/quickstart/glacier
>
> #!/bin/bash
> #PBS -S /bin/bash
>
> # Torque script for running an MPI program pn on glacier # 2005-05-26
> DSP
>
> # This presumes code compiled with the Intel compiler.
> # For example:
>
> # /global/software/mpich-1.2.5.2/ssh/bin/mpif90 pn.f -o pn
>
> #PBS -N sixsite-test
> #PBS -l walltime=240:00:00
> #PBS -l nodes=2:ppn=2
> #PBS -l qos=parallel
>
> MPIRUN="/global/software/mpich-1.2.5.2/ssh/bin/mpirun"
>
> cd $PBS_O_WORKDIR
> echo "Current working directory is `pwd`"
>
> echo "Node file: $PBS_NODEFILE :"
> echo "-"
> cat $PBS_NODEFILE
> echo "-"
> NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE` echo "Running on
> $NUM_PROCS processors."
>
> echo "Starting run at: `date`"
> ${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
> ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest echo
> "Job finished at: `date`"
>
>
>
>
>
> Payman
>
>
>
>
>
> -Original Message-
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Payman Pirzadeh
> Sent: May 19, 2009 12:36 PM
> To: 'Discussion list for GROMACS users'
> Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
>
> Dear Tsjerk,
> Thanks for your e-mail. The message that cluster sends is:
>
> "Running on 4 processors.
> Starting run at: Sat May 16 17:13:28 PDT 2009
> Warning: Command line arguments for program should be given after the
> program name. Assuming that
> ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a command line
> argument for the program.
> Warning: Command line arguments for program should be given after the
> program name. Assuming that -s is a command line argument for the
> program.
> Warning: Command line arguments for program should be given after the
> program name. Assuming that npttest is a command line argument for
> the program.
> Missing: program name
> Program -path either does not exist, is not executable, or is an
> erroneous argument to mpirun.
> Job finished at: Sat May 16 17:13:28 PDT 2009"
>
> The message that GROMACS has in log file is:
>
> "Program mdrun, VERSION 3.3.1
> Source code file: gmxfio.c, line: 706
>
> Can not open file:
> topol.tpr"
>
> This is while I have the topology file in the same folder.
>
> Payman
>
>
>
>
> -Original Message-
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Tsjerk Wassenaar
> Sent: May 19, 2009 12:25 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
>
> Hi Payman,
>
> That is probably not the only grid facility on which Gromacs may be
> run and it would be helpful if you could give specifications of it
> (WMS software e.g.), which could give you more response. Also, it
> would be helpful if you'd be able to give more information regarding
> the output. Then you'd also have to ask the question whether your
> problem is grid related or gromacs related.
[gmx-users] gromacs on glacier
Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: "In the log file of the code": There are: 1611 Atoms There are: 1611 VSites Charge group distribution at step 0: 101 147 137 152 Grid: 5 x 3 x 3 cells "in the output file reported by cluster": pwd= /home/ppirzade/GROMACS/mytests/small-box-of-water Got 4 slots. compute-1-34 compute-1-34 compute-2-20 compute-2-20 Starting run at: Mon Jun 8 10:27:52 MDT 2009 p2_22627: p4_error: Timeout in establishing connection to remote process: 0 rm_l_2_22748: (301.332031) net_send: could not write to fd=5, errno = 32 p2_22627: (301.332031) net_send: could not write to fd=5, errno = 32 p0_21851: (302.351562) net_recv failed for fd = 6 p0_21851: p4_error: net_recv read, errno = : 104 p0_21851: (306.359375) net_send: could not write to fd=4, errno = 32 Ending run at: Mon Jun 8 10:32:59 MDT 2009 "in the error file reported by cluster": Reading file npttest.tpr, VERSION 4.0.4 (single precision) Making 1D domain decomposition 4 x 1 x 1 Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energies in simulation
Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am currently using. I double-checked the parameters I gave in the .itp with TIP4P and TIP5P to make sure everything is correct in format and unit. But I can not figure out the problem. Any ideas? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energies in simulation
To the best of my knowledge no, but how can I check that? -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: June 8, 2009 11:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energies in simulation Payman Pirzadeh wrote: > Hi, > > I am using my own water model which I developed its .itp file. When > simulation is done after 1ns and energy is kinetic and potential > energies are analyzed, the kinetic value is almost OK, but the potential > energy is almost half of the value reported in literature and another MD > code that I am currently using. I double-checked the parameters I gave > in the .itp with TIP4P and TIP5P to make sure everything is correct in > format and unit. But I can not figure out the problem. Any ideas? > Is there any self-energy involved (i.e. a monomer energy that yo have to subtract)? > > > Payman > > > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energies in simulation
Here is the content of .itp file which I developed:
; This is an itp file to describe water's six-site model by H. Nada and J.P.
J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites and
3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is 111.00
degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtypecombrulegenpairsFudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name masscharge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.000.00
LW 0.00-0.044 D 0.000.00
[ moleculetype ]
;molnamenrexcl
SOL 1
[ atoms ]
; nratomtyperesnr residuename atomcgnrcharge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OWfunctiondoh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function 1
;
; site fromfunctiona b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH bonds,
a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is the
magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site fromfunctiona b c
5 1 2 3 4 -0.437172388-0.437172388
8.022961206
6 1 2 3 4 -0.437172388-0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
And here is the mdp file which I used for the simulation run:
cpp = cpp
include = -I../top
define =
; Run control
integrator = md
dt = 0.001 ;1 fs
nsteps = 100 ;10 ns
comm_mode= linear
nstcomm = 1
;Output control
nstxout = 5000
nstlog = 5000
nstenergy= 5000
nstxtcout= 1000
xtc_grps =
energygrps =
; Neighbour Searching
nstlist = 10
ns_type = grid
rlist= 0.9
; Electrostatistics
coulombtype = PME
rcoulomb = 0.9
epsilon_r= 1
; Vdw
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;Ewald
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-6
optimize_fft= yes
; Temperature coupling
tcoupl = Berendsen
tc-grps = System
tau_t= 0.1
ref_t= 300
; Pressure Coupling
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p= 1.0
compressibility = 5.5e-5
ref_p= 1.0
gen_vel = yes
The expected Potential energy is supposed to be around -41.5kJ/mol while my
potential is around -22.2kJ/mol. I calculated the energies by g_energy
command.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> To the best of my knowledge no, but how can I check that?
>
A. read the original paper: is your topology correct? Are the simulation
parameters the same?
B. post the itp file here and mdp file and specify energy and expected
energy. How about energy units?
>
> -Original Message-
> From:
RE: [gmx-users] gromacs on glacier
Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: > Hi, > > I had the chance to run the GROMACS 4.0.4 on another cluster. Same > problem still persists. But what I found is that it can be run on a node > with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . > it will crash. Following are the last lines reported in different files: > > "In the log file of the code": > > > > There are: 1611 Atoms > > There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: > p2_22627: p4_error: Timeout in establishing connection to remote process: 0 > This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html > To me, it seems that code can not communicate through more than one > node. I am suspicious of doing sth wrong during installation! I tried > wiki, but I can not find the documents as before, and I eally do not > know in which step I might have gone wrong. > If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin > > > Payman > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energies in simulation
Well, when I set the box, I used 'editconf' command to rescale the box to
have the right density which was ~997. After simulation, I got the
following:
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Density (SI)956.765150.266130.596 0.257477
257.477
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> Here is the content of .itp file which I developed:
>
> ; This is an itp file to describe water's six-site model by H. Nada and
J.P.
> J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and
> 3 Coulomb sites
> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00
> degrees, O-M and O-L are about 0.230A and 0.8892A respectively
>
> [ defaults ]
> ; non-bondedtypecombrulegenpairsFudgeLJ
> FudgeQQ N
> 1 2 NO
>
> [ atomtypes ]
> ;name masscharge ptype c6 c12
> OW 15.9994 0.0 A 0.3115 0.714845562
> HW 1.00800 0.477 A 0.0673 0.11541
> MW 0.000 -0.866 D 0.000.00
> LW 0.00-0.044 D 0.000.00
>
> [ moleculetype ]
> ;molnamenrexcl
> SOL 1
>
> [ atoms ]
> ; nratomtyperesnr residuename atomcgnrcharge
> 1 OW 1 SOL OW 1 0.0
> 2 HW 1 SOL HW1 1 0.477
> 3 HW 1 SOL HW2 1 0.477
> 4 MW 1 SOL MW 1 -0.866
> 5 LW 1 SOL LP1 1 -0.044
> 6 LW 1 SOL LP2 1 -0.044
>
> [ settles ]
> ; OWfunctiondoh dhh
> 1 1 0.0980 0.15856
>
> [ dummies3 ]
> ; These set of parameters are for M site which can be easily calculated
> using TIP4P calculations from tip4p.itp
> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
> b*(r(i)-r(k))
> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
> Remember that OM is in the same direction of OH bonds.
> ; Remember this site is in the same plane of OH bonds; so, its function 1
> ;
> ; site fromfunctiona b
> 4 1 2 3 1 0.199642536 0.199642536
>
> ; Now we define the position of L sites which can be obtained from
tip5p.itp
> ; So, it will be described as dummy site 3out: r(v) = r(i) + a*(r(i)-r(j))
+
> b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds,
> a minus sign is added. This part is similar to M site.
> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the
> magnitude of vector product of OH bonds.
> ; This sites are tetrahedral sites; so, its function 4
> ;
> ; site fromfunctiona b c
> 5 1 2 3 4 -0.437172388-0.437172388
> 8.022961206
> 6 1 2 3 4 -0.437172388-0.437172388
> -8.022961206
>
> [ exclusions ]
> 1 2 3 4 5 6
> 2 1 3 4 5 6
> 3 1 2 4 5 6
> 4 1 2 3 5 6
> 5 1 2 3 4 6
> 6 1 2 3 4 5
>
>
> And here is the mdp file which I used for the simulation run:
> cpp = cpp
> include = -I../top
> define =
>
> ; Run control
>
> integrator = md
> dt = 0.001 ;1 fs
> nsteps = 100 ;10 ns
> comm_mode= linear
> nstcomm = 1
>
> ;Output control
>
> nstxout = 5000
> nstlog = 5000
> nstenergy= 5000
> nstxtcout= 1000
> xtc_grps =
> energygrps =
>
> ; Neighbour Searching
>
> nstlist = 10
> ns_type = grid
> rlist= 0.9
>
> ; Electrostatistics
>
> coulombtype = PME
> rcoulomb = 0.9
> epsilon_r= 1
>
> ; Vdw
>
> vdwtype
RE: [gmx-users] gromacs on glacier
Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Also the gcc compiler: gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) Copyright (C) 2006 Free Software Foundation, Inc. About the system, I have water model with 3 atom sites and 3 virtual sites. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:56 AM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: > Hi Justin, > Since the manual itself was not sufficient, I asked some other people who > are running GROMACS in our group (but they run only on 2 CPUs). Here are the > steps I took to compile the parallel version (I have included my notes that > they told me as well): > > Installation > 1../configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 > This line specifies the installation path > > 2.Make > 3.Make install > These two commands will make 'grompp' and analysis functions of GROMACS. > > 4.Make clean > This command will clean some files generated during installation which are > not needed anymore. > > 5../configure --enable-mpi --disable-nice > --prefix=/global/home/pirzadeh/gromacs-4.0.4 > Here we compile the code for parallel version of GROMACS > > 6.make mdrun > 7. make install-mdrun > Now the parallel version of mdrun is built. The analysis functions are found > in 'bin' folder accompanied by 'GMXRC'. > > 8.Before running 'grompp' to produce the topology file for simulation, > we should use the command source > /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the > current code. > This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin > Sorry for tons of e-mails. > > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: June 8, 2009 11:12 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] gromacs on glacier > > > > Payman Pirzadeh wrote: >> Hi, >> >> I had the chance to run the GROMACS 4.0.4 on another cluster. Same >> problem still persists. But what I found is that it can be run on a node >> with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . >> it will crash. Following are the last lines reported in different files: >> >> "In the log file of the code": >> >> >> >> There are: 1611 Atoms >> >> There are: 1611 VSites > > All of your atoms are virtual sites? If so, I would try a simpler test > case, to > rule out stumbling across some obscure bug. > > Also: > >> p2_22627: p4_error: Timeout in establishing connection to remote process: > 0 > > This is an error message from MPICH, not Gromacs. See, for example: > > http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html > > > >> To me, it seems that code can not communicate through more than one >> node. I am suspicious of doing sth wrong during installation! I tried >> wiki, but I can not find the documents as before, and I eally do not >> know in which step I might have gone wrong. >> > > If you suspect you have done something wrong, then post the details of the > system configuration (hardware, compilers, OS, etc.) as well as a > step-by-step > record of what you did to compile the software. If your procedure is sound, > > then it helps rule out the possibility that you messed something up. > > -Justin > >> >> >> Payman >> >> >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/s
RE: [gmx-users] Energies in simulation
Well, I tried to equilibrate the system, and I think the program has
included all the distortion that the system had been through. When I checked
the trajectory, the box was highly distorted as the simulation started, then
returned to its cubic shape. Also, I am a bit confused by the word
"strange". Well, based on manual the rvdw>rlist and it is. Also, authors in
the paper have tested U with various cutoff radii from 8-11A. The results
were very close! To make sure we are on the same page, the paper address is
J. Chem. Phys., Vol118, No.16 pp7401 (2003).
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:58 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> Well, when I set the box, I used 'editconf' command to rescale the box to
> have the right density which was ~997. After simulation, I got the
> following:
>
> Energy Average RMSD Fluct. Drift
> Tot-Drift
>
> ---
> Density (SI)956.765150.266130.596 0.257477
> 257.477
The RMSD is very large. Are you sure this is in equilibrium? It could be
that your box is exploding. Please check as well that the strange twin
range cut-off that you are using is what the original authors used.
>
>
>
> Payman
>
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of David van der Spoel
> Sent: June 8, 2009 11:29 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Energies in simulation
>
> Payman Pirzadeh wrote:
>> Here is the content of .itp file which I developed:
>>
>> ; This is an itp file to describe water's six-site model by H. Nada and
> J.P.
>> J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003)
>> ; This model is a combination of TIP4P and TIP5P. It has three LJ sites
> and
>> 3 Coulomb sites
>> ; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
> 111.00
>> degrees, O-M and O-L are about 0.230A and 0.8892A respectively
>>
>> [ defaults ]
>> ; non-bondedtypecombrulegenpairsFudgeLJ
>> FudgeQQ N
>> 1 2 NO
>>
>> [ atomtypes ]
>> ;name masscharge ptype c6 c12
>> OW 15.9994 0.0 A 0.3115 0.714845562
>> HW 1.00800 0.477 A 0.0673 0.11541
>> MW 0.000 -0.866 D 0.000.00
>> LW 0.00-0.044 D 0.000.00
>>
>> [ moleculetype ]
>> ;molnamenrexcl
>> SOL 1
>>
>> [ atoms ]
>> ; nratomtyperesnr residuename atomcgnrcharge
>> 1 OW 1 SOL OW 1 0.0
>> 2 HW 1 SOL HW1 1 0.477
>> 3 HW 1 SOL HW2 1 0.477
>> 4 MW 1 SOL MW 1 -0.866
>> 5 LW 1 SOL LP1 1 -0.044
>> 6 LW 1 SOL LP2 1 -0.044
>>
>> [ settles ]
>> ; OWfunctiondoh dhh
>> 1 1 0.0980 0.15856
>>
>> [ dummies3 ]
>> ; These set of parameters are for M site which can be easily calculated
>> using TIP4P calculations from tip4p.itp
>> ; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
>> b*(r(i)-r(k))
>> ; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
>> Remember that OM is in the same direction of OH bonds.
>> ; Remember this site is in the same plane of OH bonds; so, its function 1
>> ;
>> ; site fromfunctiona b
>> 4 1 2 3 1 0.199642536 0.199642536
>>
>> ; Now we define the position of L sites which can be obtained from
> tip5p.itp
>> ; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j))
> +
>> b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
>> ; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
>> |a|=|b|=const/2. since the lone pairs are in opposite direction of OH
> bonds,
>> a minus sign is added. This part is similar to M site.
>> ; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
> the
>> magnitude of vector product of OH bonds.
>> ; This sites are tetrahedral sites;
RE: [gmx-users] gromacs on glacier
Hi Justin, Regarding your suggestion using spc216, when I tried the energetically minimize spc216 with grompp,I got the following error: Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File spce.itp, line 1 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype Same thing happened when I tried TIP4P. Where is the problem? I did not have this issue with my own model. Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 1:53 PM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: > Dear Justin, > Here is the mpich version: > MPICH Version: 1.2.7p1 > MPICH Release date: $Date: 2005/11/04 11:54:51$ > MPICH Patches applied: none > MPICH configure:-prefix=/share/apps/intel/mpich/ > MPICH Device: ch_p4 > Well, I think that MPICH is your problem then. There are several reports of sporadic bugs (the one that you're seeing!) with that version. Since it's several years old, getting a fix is probably a bit unlikely :) Perhaps you can sort out with the sysadmins what you can do. Like I said before, probably OpenMPI is a better bet - we've never had a problem with it. You can probably install it yourself in your home directory, and point to mpicc with environment variables during the Gromacs installation. > Also the gcc compiler: > gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) > Copyright (C) 2006 Free Software Foundation, Inc. > > About the system, I have water model with 3 atom sites and 3 virtual sites. > Probably not a very good test case for diagnosing problems, but I think it's unrelated in this case. When testing, keep it simple - run a simulation with spc216.gro from the Gromacs installation, it should pretty much always work :) -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: June 8, 2009 11:56 AM > To: Gromacs Users' List > Subject: Re: [gmx-users] gromacs on glacier > > > > Payman Pirzadeh wrote: >> Hi Justin, >> Since the manual itself was not sufficient, I asked some other people who >> are running GROMACS in our group (but they run only on 2 CPUs). Here are > the >> steps I took to compile the parallel version (I have included my notes > that >> they told me as well): >> >> Installation >> 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 >> This line specifies the installation path >> >> 2. Make >> 3. Make install >> These two commands will make 'grompp' and analysis functions of GROMACS. >> >> 4. Make clean >> This command will clean some files generated during installation which are >> not needed anymore. >> >> 5. ./configure --enable-mpi --disable-nice >> --prefix=/global/home/pirzadeh/gromacs-4.0.4 >> Here we compile the code for parallel version of GROMACS >> >> 6. make mdrun >> 7.make install-mdrun >> Now the parallel version of mdrun is built. The analysis functions are > found >> in 'bin' folder accompanied by 'GMXRC'. >> >> 8. Before running 'grompp' to produce the topology file for simulation, >> we should use the command source >> /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the >> current code. >> > > This is pretty much the standard installation procedure. What we also need > to > know are the compilers used, etc. for the installation. The error you're > getting is from MPICH. Which version is installed on the cluster? It may > be > old and buggy. In any case, you can try to install something newer, like a > recent version of OpenMPI (which we have on our cluster); it may be more > reliable. Only a random thought, means nothing unless we know what you have > > installed :) > > What about the contents of your system, as I asked before? Do you really > have a > 100% virtual site system? > > -Justin > >> Sorry for tons of e-mails. >> >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: June 8, 2009 11:12 AM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] gromacs on glacier >> >> >> >> Payman Pirzadeh wrote: >>> Hi, >>> >>> I had the chance to run the GROMACS 4.0.4 on another cluster. Sa
[gmx-users] making a box of water
Hello, I am trying to make a box of water from three different water models. I can make one from my own water model, but when I want to test TIP4P and SPCE, as soon as it comes to energy minimization step and using grompp, I get the following error message: Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File spce.itp, line 1 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype What is the problem causing the code referring to itp file? Regards, Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] making a box of water
Here is my .top file: ;This includes SPC-E potential #include "spce.itp" [ system ] Pure box of water [ molecules ] SOL 515 I used the same thing with my own model, but it had worked. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 6:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Hello, > > I am trying to make a box of water from three different water models. I > can make one from my own water model, but when I want to test TIP4P and > SPCE, as soon as it comes to energy minimization step and using grompp, > I get the following error message: > > > > Program grompp, VERSION 4.0.4 > > Source code file: topio.c, line: 415 > > > > Fatal error: > > Syntax error - File spce.itp, line 1 > > Last line read: > > '[ moleculetype ]' > > Invalid order for directive moleculetype > > > > What is the problem causing the code referring to itp file? > See the message I just sent. Something is out of order in your .top file. -Justin > Regards, > > > > Payman > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] making a box of water
Will #include "ffgmx.itp" solve my problem? Would it be a general solution or in each case I should specify (if I add other solutes such as proteins)? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:07 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water You need to #include an appropriate force field that contains the [defaults], [atomtypes], etc. before you can define a [moleculetype]. -Justin Payman Pirzadeh wrote: > Here is my .top file: > > ;This includes SPC-E potential > #include "spce.itp" > > [ system ] > Pure box of water > > [ molecules ] > SOL 515 > > I used the same thing with my own model, but it had worked. > > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 14, 2009 6:54 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> Hello, >> >> I am trying to make a box of water from three different water models. I >> can make one from my own water model, but when I want to test TIP4P and >> SPCE, as soon as it comes to energy minimization step and using grompp, >> I get the following error message: >> >> >> >> Program grompp, VERSION 4.0.4 >> >> Source code file: topio.c, line: 415 >> >> >> >> Fatal error: >> >> Syntax error - File spce.itp, line 1 >> >> Last line read: >> >> '[ moleculetype ]' >> >> Invalid order for directive moleculetype >> >> >> >> What is the problem causing the code referring to itp file? >> > > See the message I just sent. Something is out of order in your .top file. > > -Justin > >> Regards, >> >> >> >> Payman >> >> >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] making a box of water
OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairsFudgeLJ FudgeQQ N 1 2 NO ; include TIP4P topology #include "tip4p.itp" [ system ] Pure box of water [ molecules ] SOL 506 But I still get the same error message! Should I include the [defaults] in the .itp file? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:56 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Will #include "ffgmx.itp" solve my problem? Would it be a general solution > or in each case I should specify (if I add other solutes such as proteins)? > Well, ffgmx is deprecated, so it is probably not the best choice :) Choosing a force field should not be a haphazard occasion, it is a very important choice. For water models, parameters should be uniform, but if you're simulating a protein, you'll want to make a very educated decision. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 14, 2009 7:07 PM > To: Gromacs Users' List > Subject: Re: [gmx-users] making a box of water > > > You need to #include an appropriate force field that contains the > [defaults], > [atomtypes], etc. before you can define a [moleculetype]. > > -Justin > > Payman Pirzadeh wrote: >> Here is my .top file: >> >> ;This includes SPC-E potential >> #include "spce.itp" >> >> [ system ] >> Pure box of water >> >> [ molecules ] >> SOL 515 >> >> I used the same thing with my own model, but it had worked. >> >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 14, 2009 6:54 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Hello, >>> >>> I am trying to make a box of water from three different water models. I >>> can make one from my own water model, but when I want to test TIP4P and >>> SPCE, as soon as it comes to energy minimization step and using grompp, >>> I get the following error message: >>> >>> >>> >>> Program grompp, VERSION 4.0.4 >>> >>> Source code file: topio.c, line: 415 >>> >>> >>> >>> Fatal error: >>> >>> Syntax error - File spce.itp, line 1 >>> >>> Last line read: >>> >>> '[ moleculetype ]' >>> >>> Invalid order for directive moleculetype >>> >>> >>> >>> What is the problem causing the code referring to itp file? >>> >> See the message I just sent. Something is out of order in your .top file. >> >> -Justin >> >>> Regards, >>> >>> >>> >>> Payman >>> >>> >>> >>> >>> >>> >>> ___ >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before > posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] making a box of water
Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms ]are specifies as opls_???, doesn't grompp check the database for the corresponding parameters? Or we should again manually specify the [ atomtypes ] again in either .itp or .top file? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairsFudgeLJ FudgeQQ N 1 2 NO ; include TIP4P topology #include "tip4p.itp" [ system ] Pure box of water [ molecules ] SOL 506 But I still get the same error message! Should I include the [defaults] in the .itp file? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:56 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Will #include "ffgmx.itp" solve my problem? Would it be a general solution > or in each case I should specify (if I add other solutes such as proteins)? > Well, ffgmx is deprecated, so it is probably not the best choice :) Choosing a force field should not be a haphazard occasion, it is a very important choice. For water models, parameters should be uniform, but if you're simulating a protein, you'll want to make a very educated decision. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 14, 2009 7:07 PM > To: Gromacs Users' List > Subject: Re: [gmx-users] making a box of water > > > You need to #include an appropriate force field that contains the > [defaults], > [atomtypes], etc. before you can define a [moleculetype]. > > -Justin > > Payman Pirzadeh wrote: >> Here is my .top file: >> >> ;This includes SPC-E potential >> #include "spce.itp" >> >> [ system ] >> Pure box of water >> >> [ molecules ] >> SOL 515 >> >> I used the same thing with my own model, but it had worked. >> >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 14, 2009 6:54 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Hello, >>> >>> I am trying to make a box of water from three different water models. I >>> can make one from my own water model, but when I want to test TIP4P and >>> SPCE, as soon as it comes to energy minimization step and using grompp, >>> I get the following error message: >>> >>> >>> >>> Program grompp, VERSION 4.0.4 >>> >>> Source code file: topio.c, line: 415 >>> >>> >>> >>> Fatal error: >>> >>> Syntax error - File spce.itp, line 1 >>> >>> Last line read: >>> >>> '[ moleculetype ]' >>> >>> Invalid order for directive moleculetype >>> >>> >>> >>> What is the problem causing the code referring to itp file? >>> >> See the message I just sent. Something is out of order in your .top file. >> >> -Justin >> >>> Regards, >>> >>> >>> >>> Payman >>> >>> >>> >>> >>> >>> >>> ___ >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before > posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/ju
RE: [gmx-users] making a box of water
Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Hi again, > I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in > the [atoms ]are specifies as opls_???, doesn't grompp check the database > for the corresponding parameters? Or we should again manually specify the [ > atomtypes ] again in either .itp or .top file? > You need to #include "ffoplsaa.itp" to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Payman Pirzadeh > Sent: July 15, 2009 10:14 AM > To: jalem...@vt.edu; 'Discussion list for GROMACS users' > Subject: RE: [gmx-users] making a box of water > > OK! > I changed my .top file to > > ;This is simulation for TIP4P water model > [ defaults ] > ; non-bondedtypecombrulegenpairsFudgeLJ > FudgeQQ N > 1 2 NO > > ; include TIP4P topology > #include "tip4p.itp" > > [ system ] > Pure box of water > > [ molecules ] > SOL 506 > > But I still get the same error message! Should I include the [defaults] in > the .itp file? > > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 14, 2009 7:56 PM > To: Gromacs Users' List > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> Will #include "ffgmx.itp" solve my problem? Would it be a general solution >> or in each case I should specify (if I add other solutes such as > proteins)? > > Well, ffgmx is deprecated, so it is probably not the best choice :) > Choosing a > force field should not be a haphazard occasion, it is a very important > choice. > For water models, parameters should be uniform, but if you're simulating a > protein, you'll want to make a very educated decision. > > -Justin > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 14, 2009 7:07 PM >> To: Gromacs Users' List >> Subject: Re: [gmx-users] making a box of water >> >> >> You need to #include an appropriate force field that contains the >> [defaults], >> [atomtypes], etc. before you can define a [moleculetype]. >> >> -Justin >> >> Payman Pirzadeh wrote: >>> Here is my .top file: >>> >>> ;This includes SPC-E potential >>> #include "spce.itp" >>> >>> [ system ] >>> Pure box of water >>> >>> [ molecules ] >>> SOL 515 >>> >>> I used the same thing with my own model, but it had worked. >>> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Justin A. Lemkul >>> Sent: July 14, 2009 6:54 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] making a box of water >>> >>> >>> >>> Payman Pirzadeh wrote: >>>> Hello, >>>> >>>> I am trying to make a box of water from three different water models. I >>>> can make one from my own water model, but when I want to test TIP4P and >>>> SPCE, as soon as it comes to energy minimization step and using grompp, >>>> I get the following error message: >>>> >>>> >>>> >>>> Program grompp, VERSION 4.0.4 >>>> >>>> Source code file: topio.c, line: 415 >>>> >>>> >>>&g
[gmx-users] Energy of a box of water
Hi, I tested TIP4P and SPC-E. I used the .gro files in /share/top of the gromacs. The outputs of energy are: TIP4P, 1ns npT, T=300K Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-20929115.164113.745 0.0624384 62.4385 Kinetic En. 3781.572.906172.4712 0.0275462 27.5462 Total Energy -17147.598.1701 94.671 0.0899847 89.9848 Temperature 299.9065.78209 5.7476 0.00218465 2.18465 Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000371707) SPC-E, npT, T= 300K Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -24058.6114.598109.211 0.120286 120.287 Kinetic En. 3848.77 73.86273.7792 -0.0121097 -12.1097 Total Energy -20209.995.404290.1487 0.108177 108.177 The potential energies are again half of what they should be! Exactly the same problem with my own six-site model. Initially I thought I might have done sth in my .itp file, but now, I really do not understand where the problem comes from Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Thanks Justin. > Unfortunately, I realized that after I sent the e-mail. Anyways, I started > running to models: SPCE and TIP4P to check the energies of these systems to > figure out where the problem with my own system (six-site model) could be. I > will keep you posted. But, I have a question about the compressibility > factor used in .mdp file. Does that(if it is not a correct value) truly > affect the simulation when the reference pressure is set? > No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 15, 2009 11:38 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> Hi again, >> I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes > in >> the [atoms ]are specifies as opls_???, doesn't grompp check the database >> for the corresponding parameters? Or we should again manually specify the > [ >> atomtypes ] again in either .itp or .top file? >> > > You need to #include "ffoplsaa.itp" to take care of everything related to > the > OPLS-AA force field. Invoking grompp is not magic, the topology has to > contain > specific instructions for everything you need to handle in your system. > > -Justin > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Payman Pirzadeh >> Sent: July 15, 2009 10:14 AM >> To: jalem...@vt.edu; 'Discussion list for GROMACS users' >> Subject: RE: [gmx-users] making a box of water >> >> OK! >> I changed my .top file to >> >> ;This is simulation for TIP4P water model >> [ defaults ] >> ; non-bondedtypecombrulegenpairsFudgeLJ >> FudgeQQ N >> 1 2 NO >> >> ; include TIP4P topology >> #include "tip4p.itp" >> >> [ system ] >> Pure box of water >> >> [ molecules ] >> SOL 506 >> >> But I still get the same error message! Should I include the [defaults] in >> the .itp file? >> >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 14, 2009 7:56 PM >> To: Gromacs Users' List >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Will #include "ffgmx.itp" solve my problem? Would it be a general > solution >>> or in each case I should specify (if I add other solutes such as >> proteins)? >> >> Well, ffgmx is deprecated, so it is probably not the best choice :) >> Choosing a >> force field should not be a haphazard occasion, it is a very important >> choice. >> For water models, parameters should be u
RE: [gmx-users] Energy of a box of water
-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 2:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy of a box of water Payman Pirzadeh wrote: > Hi, > I tested TIP4P and SPC-E. I used the .gro files in /share/top of the > gromacs. The outputs of energy are: > > TIP4P, 1ns npT, T=300K > > Energy Average RMSD Fluct. Drift > Tot-Drift > > --- > Potential-20929115.164113.745 0.0624384 > 62.4385 > Kinetic En. 3781.572.906172.4712 0.0275462 > 27.5462 > Total Energy -17147.598.1701 94.671 0.0899847 > 89.9848 > Temperature 299.9065.78209 5.7476 0.00218465 > 2.18465 > Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000371707) > > > SPC-E, npT, T= 300K > > Energy Average RMSD Fluct. Drift > Tot-Drift > > --- > Potential -24058.6114.598109.211 0.120286 > 120.287 > Kinetic En. 3848.77 73.86273.7792 -0.0121097 > -12.1097 > Total Energy -20209.995.404290.1487 0.108177 > 108.177 > > The potential energies are again half of what they should be! Exactly the > same problem with my own six-site model. Initially I thought I might have > done sth in my .itp file, but now, I really do not understand where the > problem comes from If these boxes contain 512 molecules that means the energy is -42 kJ/mol for TIP4P and slightly lower for SPC/E. Exactly correct. However the distribution contains boxes with 216 molecules, which makes that this is way too low, it should be -9000 for TIP4P. How many molecules do you have? Based on the topology files, I have 515 molecules for SPCE and 506 for TIP4P. have 515 molecules for SPCE and 506 for TIP4P. > > Payman > > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of David van der Spoel > Sent: July 15, 2009 12:23 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > Payman Pirzadeh wrote: >> Thanks Justin. >> Unfortunately, I realized that after I sent the e-mail. Anyways, I started >> running to models: SPCE and TIP4P to check the energies of these systems > to >> figure out where the problem with my own system (six-site model) could be. > I >> will keep you posted. But, I have a question about the compressibility >> factor used in .mdp file. Does that(if it is not a correct value) truly >> affect the simulation when the reference pressure is set? >> > No, only the relaxation rate (with Berendsen scaling) resp. the > oscillation period with Parrinello Rahman. > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 15, 2009 11:38 AM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Hi again, >>> I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes >> in >>> the [atoms ]are specifies as opls_???, doesn't grompp check the database >>> for the corresponding parameters? Or we should again manually specify the >> [ >>> atomtypes ] again in either .itp or .top file? >>> >> You need to #include "ffoplsaa.itp" to take care of everything related to >> the >> OPLS-AA force field. Invoking grompp is not magic, the topology has to >> contain >> specific instructions for everything you need to handle in your system. >> >> -Justin >> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Payman Pirzadeh >>> Sent: July 15, 2009 10:14 AM >>> To: jalem...@vt.edu; 'Discussion list for GROMACS users' >>> Subject: RE: [gmx-users] making a box of water >>> >>> OK! >>> I changed my .top file to >>> >>> ;This is simulation for TIP4P water model >>> [ defaults ] >>> ; non-bondedtypecombrulegenpairsFudgeLJ >>> FudgeQQ N >>> 1
RE: [gmx-users] Energy of a box of water
-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 2:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy of a box of water Payman Pirzadeh wrote: > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of David van der Spoel > Sent: July 15, 2009 2:26 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Energy of a box of water > > Payman Pirzadeh wrote: >> Hi, >> I tested TIP4P and SPC-E. I used the .gro files in /share/top of the >> gromacs. The outputs of energy are: >> >> TIP4P, 1ns npT, T=300K >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> > >> --- >> Potential-20929115.164113.745 0.0624384 >> 62.4385 >> Kinetic En. 3781.572.906172.4712 0.0275462 >> 27.5462 >> Total Energy -17147.598.1701 94.671 0.0899847 >> 89.9848 >> Temperature 299.9065.78209 5.7476 0.00218465 >> 2.18465 >> Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000371707) >> >> >> SPC-E, npT, T= 300K >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> > >> --- >> Potential -24058.6114.598109.211 0.120286 >> 120.287 >> Kinetic En. 3848.77 73.86273.7792 -0.0121097 >> -12.1097 >> Total Energy -20209.995.404290.1487 0.108177 >> 108.177 >> >> The potential energies are again half of what they should be! Exactly the >> same problem with my own six-site model. Initially I thought I might have >> done sth in my .itp file, but now, I really do not understand where the >> problem comes from > > If these boxes contain 512 molecules that means the energy is -42 kJ/mol > for TIP4P and slightly lower for SPC/E. Exactly correct. > However the distribution contains boxes with 216 molecules, which makes > that this is way too low, it should be -9000 for TIP4P. > > How many molecules do you have? > > > Based on the topology files, I have 515 molecules for SPCE and 506 for > TIP4P. have 515 molecules for SPCE and 506 for TIP4P. Then it is fine. Which energy do you get for your own model? These are the results I got. It includes all the initial equilibration time during which simulation box got distorted. Energy Average RMSDFluct. Drift Tot-Drift --- Potential -21955.7739.133 538.245 -1.7548 -1754.8 Kinetic 4015.45 105.699 98.5134 -0.132693 -132.693 Total -17940.3775.785 552.229 -1.88749-1887.49 If I ignore that piece of trajectory, then the average will be 22174.95. But, I can not understand how these values are fine? What is the connection between the values in the tables and the literature values (~-40kJ/mol)? I am truly confused!!! > > > > > > >> Payman >> >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of David van der Spoel >> Sent: July 15, 2009 12:23 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] making a box of water >> >> Payman Pirzadeh wrote: >>> Thanks Justin. >>> Unfortunately, I realized that after I sent the e-mail. Anyways, I > started >>> running to models: SPCE and TIP4P to check the energies of these systems >> to >>> figure out where the problem with my own system (six-site model) could > be. >> I >>> will keep you posted. But, I have a question about the compressibility >>> factor used in .mdp file. Does that(if it is not a correct value) truly >>> affect the simulation when the reference pressure is set? >>> >> No, only the relaxation rate (with Berendsen scaling) resp. the >> oscillation period with Parrinello Rahman. >> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Justin A. Lemkul >>> Sent: July 15, 2009 11:38 AM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] makin
RE: [gmx-users] Energy of a box of water
Thanks a lot That was a big clarification and relief So, my model is working! Since the RDFs are also correct! Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 2:50 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy of a box of water Payman Pirzadeh wrote: > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of David van der Spoel > Sent: July 15, 2009 2:38 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Energy of a box of water > > Payman Pirzadeh wrote: >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of David van der Spoel >> Sent: July 15, 2009 2:26 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Energy of a box of water >> >> Payman Pirzadeh wrote: >>> Hi, >>> I tested TIP4P and SPC-E. I used the .gro files in /share/top of the >>> gromacs. The outputs of energy are: >>> >>> TIP4P, 1ns npT, T=300K >>> >>> Energy Average RMSD Fluct. Drift >>> Tot-Drift >>> > >>> --- >>> Potential-20929115.164113.745 0.0624384 >>> 62.4385 >>> Kinetic En. 3781.572.906172.4712 0.0275462 >>> 27.5462 >>> Total Energy -17147.598.1701 94.671 0.0899847 >>> 89.9848 >>> Temperature 299.9065.78209 5.7476 0.00218465 >>> 2.18465 >>> Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000371707) >>> >>> >>> SPC-E, npT, T= 300K >>> >>> Energy Average RMSD Fluct. Drift >>> Tot-Drift >>> > >>> --- >>> Potential -24058.6114.598109.211 0.120286 >>> 120.287 >>> Kinetic En. 3848.77 73.86273.7792 -0.0121097 >>> -12.1097 >>> Total Energy -20209.995.404290.1487 0.108177 >>> 108.177 >>> >>> The potential energies are again half of what they should be! Exactly the >>> same problem with my own six-site model. Initially I thought I might have >>> done sth in my .itp file, but now, I really do not understand where the >>> problem comes from >> If these boxes contain 512 molecules that means the energy is -42 kJ/mol >> for TIP4P and slightly lower for SPC/E. Exactly correct. >> However the distribution contains boxes with 216 molecules, which makes >> that this is way too low, it should be -9000 for TIP4P. >> >> How many molecules do you have? >> >> >> Based on the topology files, I have 515 molecules for SPCE and 506 for >> TIP4P. have 515 molecules for SPCE and 506 for TIP4P. > > Then it is fine. Which energy do you get for your own model? > > > These are the results I got. It includes all the initial equilibration time > during which simulation box got distorted. > > EnergyAverage RMSDFluct. Drift Tot-Drift > > --- > Potential -21955.7739.133 538.245 -1.7548 -1754.8 > Kinetic 4015.45 105.699 98.5134 -0.132693 -132.693 > Total -17940.3775.785 552.229 -1.88749-1887.49 > > If I ignore that piece of trajectory, then the average will be 22174.95. > But, I can not understand how these values are fine? What is the connection > between the values in the tables and the literature values (~-40kJ/mol)? I > am truly confused!!! You have to divide by the number of molecules. g_energy -nmol N > > > >> >> >> >> >> >>> Payman >>> >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of David van der Spoel >>> Sent: July 15, 2009 12:23 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] making a box of water >>> >>> Payman Pirzadeh wrote: >>>> Thanks Justin. >>>> Unfortunately, I realized that after I sent the e-mail. Anyways, I >> started >>>>
[gmx-users] making a box of water
Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Thanks Justin. > Unfortunately, I realized that after I sent the e-mail. Anyways, I started > running to models: SPCE and TIP4P to check the energies of these systems to > figure out where the problem with my own system (six-site model) could be. I > will keep you posted. But, I have a question about the compressibility > factor used in .mdp file. Does that(if it is not a correct value) truly > affect the simulation when the reference pressure is set? > No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 15, 2009 11:38 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> Hi again, >> I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes > in >> the [atoms ]are specifies as opls_???, doesn't grompp check the database >> for the corresponding parameters? Or we should again manually specify the > [ >> atomtypes ] again in either .itp or .top file? >> > > You need to #include "ffoplsaa.itp" to take care of everything related to > the > OPLS-AA force field. Invoking grompp is not magic, the topology has to > contain > specific instructions for everything you need to handle in your system. > > -Justin > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Payman Pirzadeh >> Sent: July 15, 2009 10:14 AM >> To: jalem...@vt.edu; 'Discussion list for GROMACS users' >> Subject: RE: [gmx-users] making a box of water >> >> OK! >> I changed my .top file to >> >> ;This is simulation for TIP4P water model >> [ defaults ] >> ; non-bondedtypecombrulegenpairsFudgeLJ >> FudgeQQ N >> 1 2 NO >> >> ; include TIP4P topology >> #include "tip4p.itp" >> >> [ system ] >> Pure box of water >> >> [ molecules ] >> SOL 506 >> >> But I still get the same error message! Should I include the [defaults] in >> the .itp file? >> >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 14, 2009 7:56 PM >> To: Gromacs Users' List >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Will #include "ffgmx.itp" solve my problem? Would it be a general > solution >>> or in each case I should specify (if I add other solutes such as >> proteins)? >> >> Well, ffgmx is deprecated, so it is probably not the best choice :) >> Choosing a >> force field should not be a haphazard occasion, it is a very important >> choice. >> For water models, parameters should be uniform, but if you're simulating a > >> protein, you'll want to make a very educated decision. >> >> -Justin >> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Justin A. Lemkul >>> Sent: July 14, 2009 7:07 PM >>> To: Gromacs Users' List >>> Subject: Re: [gmx-users] making a box of water >>> >>> >>> You need to #include an appropriate force field that contains the >>> [defaults], >>> [atomtypes], etc. before you can define a [moleculetype]. >>> >>> -Justin >>> >>> Payman Pirzadeh wrote: >>>> Here is my .top
RE: [gmx-users] making a box of water
I forgot to mention, the dimensions of current simulation box are: 27.154A* 31.354A* 103.386A Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 7:24 PM To: 'Discussion list for GROMACS users' Subject: [gmx-users] making a box of water Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Thanks Justin. > Unfortunately, I realized that after I sent the e-mail. Anyways, I started > running to models: SPCE and TIP4P to check the energies of these systems to > figure out where the problem with my own system (six-site model) could be. I > will keep you posted. But, I have a question about the compressibility > factor used in .mdp file. Does that(if it is not a correct value) truly > affect the simulation when the reference pressure is set? > No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 15, 2009 11:38 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> Hi again, >> I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes > in >> the [atoms ]are specifies as opls_???, doesn't grompp check the database >> for the corresponding parameters? Or we should again manually specify the > [ >> atomtypes ] again in either .itp or .top file? >> > > You need to #include "ffoplsaa.itp" to take care of everything related to > the > OPLS-AA force field. Invoking grompp is not magic, the topology has to > contain > specific instructions for everything you need to handle in your system. > > -Justin > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Payman Pirzadeh >> Sent: July 15, 2009 10:14 AM >> To: jalem...@vt.edu; 'Discussion list for GROMACS users' >> Subject: RE: [gmx-users] making a box of water >> >> OK! >> I changed my .top file to >> >> ;This is simulation for TIP4P water model >> [ defaults ] >> ; non-bondedtypecombrulegenpairsFudgeLJ >> FudgeQQ N >> 1 2 NO >> >> ; include TIP4P topology >> #include "tip4p.itp" >> >> [ system ] >> Pure box of water >> >> [ molecules ] >> SOL 506 >> >> But I still get the same error message! Should I include the [defaults] in >> the .itp file? >> >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 14, 2009 7:56 PM >> To: Gromacs Users' List >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Will #include "ffgmx.itp" solve my problem? Would it be a general > solution >>> or in each case I should specify (if I add other solutes such as >> proteins)? >> >> Well, ffgmx is deprecated, so it is probably not the best choice :) >> Choosing a >> force field should not be a haphazard occasion, it is a very important >> choice. >> For water models, parameters should be uniform, but if you're simulating a > >> protein, you'll want to make a very educated decision. >> >> -Justin >> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Justin A. Lemkul >>> Sent: July 14, 2009 7:07 PM >>> To: Gromacs Users' List >>> Subjec
RE: [gmx-users] making a box of water
Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Hello, > I have an .pdb file from another simulation. I want to make the appropriate > input files to run a simulations. I have used grompp to produce the .tpr > file, but I get the usual ERROR: > > ERROR: The cut-off length is longer than half the shortest box vector or > longer than the smallest box diagonal element. Increase the box size or > decrease rvdw. > > I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still > the problem persists! Smaller rvdw is not good for my system. Any > suggestions? > Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of David van der Spoel > Sent: July 15, 2009 12:23 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > Payman Pirzadeh wrote: >> Thanks Justin. >> Unfortunately, I realized that after I sent the e-mail. Anyways, I started >> running to models: SPCE and TIP4P to check the energies of these systems > to >> figure out where the problem with my own system (six-site model) could be. > I >> will keep you posted. But, I have a question about the compressibility >> factor used in .mdp file. Does that(if it is not a correct value) truly >> affect the simulation when the reference pressure is set? >> > No, only the relaxation rate (with Berendsen scaling) resp. the > oscillation period with Parrinello Rahman. > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 15, 2009 11:38 AM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Hi again, >>> I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes >> in >>> the [atoms ]are specifies as opls_???, doesn't grompp check the database >>> for the corresponding parameters? Or we should again manually specify the >> [ >>> atomtypes ] again in either .itp or .top file? >>> >> You need to #include "ffoplsaa.itp" to take care of everything related to >> the >> OPLS-AA force field. Invoking grompp is not magic, the topology has to >> contain >> specific instructions for everything you need to handle in your system. >> >> -Justin >> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Payman Pirzadeh >>> Sent: July 15, 2009 10:14 AM >>> To: jalem...@vt.edu; 'Discussion list for GROMACS users' >>> Subject: RE: [gmx-users] making a box of water >>> >>> OK! >>> I changed my .top file to >>> >>> ;This is simulation for TIP4P water model >>> [ defaults ] >>> ; non-bondedtypecombrulegenpairsFudgeLJ >>> FudgeQQ N >>> 1 2 NO >>> >>> ; include TIP4P topology >>> #include "tip4p.itp" >>> >>> [ system ] >>> Pure box of water >>> >>> [ molecules ] >>> SOL 506 >>> >>> But I still get the same error message! Should I include the [defaults] > in >>> the .itp file? >>> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Justin A. Lemkul >>> Sent: July 14, 2009 7:56 PM >>> To: Gromacs Users' List >>> Subject: Re: [gmx-users] making a box of water >>> >>> >>> >>> Payman Pirzadeh wrote: >>>> Will #include "ffgmx.itp" solve my
RE: [gmx-users] making a box of water
But, I am using a .pdb file as the input of the gromacs. Does the preparation of pdb file differ from software to software? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 11:42 AM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Hello, > Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the > rvdw cutoff to 10A, but problem was still there. > Now I made my box bigger by using a visualization software. The new > dimensions are ~54*63*103.38(all in A). Again the same warning is given to > me about increasing the box size or reduce the rvdw. > Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 15, 2009 7:32 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> Hello, >> I have an .pdb file from another simulation. I want to make the > appropriate >> input files to run a simulations. I have used grompp to produce the .tpr >> file, but I get the usual ERROR: >> >> ERROR: The cut-off length is longer than half the shortest box vector or >> longer than the smallest box diagonal element. Increase the box size or >> decrease rvdw. >> >> I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still >> the problem persists! Smaller rvdw is not good for my system. Any >> suggestions? >> > > Then you'll have to use a bigger box, most likely. What is your smallest > box > vector? That should indicate the limits of your cutoffs. > > -Justin > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of David van der Spoel >> Sent: July 15, 2009 12:23 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] making a box of water >> >> Payman Pirzadeh wrote: >>> Thanks Justin. >>> Unfortunately, I realized that after I sent the e-mail. Anyways, I > started >>> running to models: SPCE and TIP4P to check the energies of these systems >> to >>> figure out where the problem with my own system (six-site model) could > be. >> I >>> will keep you posted. But, I have a question about the compressibility >>> factor used in .mdp file. Does that(if it is not a correct value) truly >>> affect the simulation when the reference pressure is set? >>> >> No, only the relaxation rate (with Berendsen scaling) resp. the >> oscillation period with Parrinello Rahman. >> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Justin A. Lemkul >>> Sent: July 15, 2009 11:38 AM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] making a box of water >>> >>> >>> >>> Payman Pirzadeh wrote: >>>> Hi again, >>>> I have a question about the .itp files. When e.g. TIP4P.itp the > atomtypes >>> in >>>> the [atoms ]are specifies as opls_???, doesn't grompp check the > database >>>> for the corresponding parameters? Or we should again manually specify > the >>> [ >>>> atomtypes ] again in either .itp or .top file? >>>> >>> You need to #include "ffoplsaa.itp" to take care of everything related to >>> the >>> OPLS-AA force field. Invoking grompp is not magic, the topology has to >>> contain >>> specific instructions for everything you need to handle in your system. >>> >>> -Justin >>> >>>> Payman >>>> >>>> -Original Message- >>>> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] >>>> On Behalf Of Payman Pirzadeh >>>> Sent: July 15, 2009 10:14 AM >>>> To: jalem...@vt.edu; 'Discussion list for GROMACS users' >>>> Subject: RE: [gmx-users] making a box of water >>>> >>>> OK! >&g
RE: [gmx-users] making a box of water
You were right! The dimensions of the box are zero in the .gro file. Should I change them to the values I have? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:08 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > But, I am using a .pdb file as the input of the gromacs. Does the > preparation of pdb file differ from software to software? > It shouldn't, and I'm not 100% sure on how Gromacs handles system size from a .pdb file (I always use .gro). What you can try to do is transform your .pdb into .gro format with editconf, and read the last line of the .gro file. That's any easy way to determine the size of the box Gromacs is finding. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 16, 2009 11:42 AM > To: Gromacs Users' List > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> Hello, >> Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the >> rvdw cutoff to 10A, but problem was still there. >> Now I made my box bigger by using a visualization software. The new >> dimensions are ~54*63*103.38(all in A). Again the same warning is given to >> me about increasing the box size or reduce the rvdw. >> > > Well, Gromacs doesn't do anything in A, it's all nm, so be sure that > everything > you're doing is consistent with Gromacs conventions. There is no reason > that > either of those boxe should be complaining about a 1.0-nm cutoff, so there > has > to be something that messed up along the way. > > -Justin > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 15, 2009 7:32 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Hello, >>> I have an .pdb file from another simulation. I want to make the >> appropriate >>> input files to run a simulations. I have used grompp to produce the .tpr >>> file, but I get the usual ERROR: >>> >>> ERROR: The cut-off length is longer than half the shortest box vector or >>> longer than the smallest box diagonal element. Increase the box size or >>> decrease rvdw. >>> >>> I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still >>> the problem persists! Smaller rvdw is not good for my system. Any >>> suggestions? >>> >> Then you'll have to use a bigger box, most likely. What is your smallest >> box >> vector? That should indicate the limits of your cutoffs. >> >> -Justin >> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of David van der Spoel >>> Sent: July 15, 2009 12:23 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] making a box of water >>> >>> Payman Pirzadeh wrote: >>>> Thanks Justin. >>>> Unfortunately, I realized that after I sent the e-mail. Anyways, I >> started >>>> running to models: SPCE and TIP4P to check the energies of these systems >>> to >>>> figure out where the problem with my own system (six-site model) could >> be. >>> I >>>> will keep you posted. But, I have a question about the compressibility >>>> factor used in .mdp file. Does that(if it is not a correct value) truly >>>> affect the simulation when the reference pressure is set? >>>> >>> No, only the relaxation rate (with Berendsen scaling) resp. the >>> oscillation period with Parrinello Rahman. >>> >>>> Payman >>>> >>>> -Original Message- >>>> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] >>>> On Behalf Of Justin A. Lemkul >>>> Sent: July 15, 2009 11:38 AM >>>> To: Discussion list for GROMACS users >>>> Subject: Re: [gmx-users] making a box of water >>>> >>>> >>>> >>>> Payman Pirzadeh wrote: >>>>> Hi again, >>>>> I have a question about the .itp files. When
[gmx-users] minimzation problem with a heterogeneous system
Hello, I have a configuration in which half of the box is liquid water and the other half is ice. This configuration is the output of another simulation in which the mentioned config worked (and still works fine). But when I start minimizing it (I started minimization since my first round of MD run crashed due to messages indicative of clashes). But minimation ends with the following message: Steepest Descents: Tolerance (Fmax) = 1.0e-06 Number of steps= 50 Step=1, Dmax= 1.0e-01 nm, Epot= 6.09464e+11 Fmax= 1.31718e+14, atom= 2938 Step=2, Dmax= 1.2e-01 nm, Epot= 1.15027e+09 Fmax= 2.00242e+11, atom= 2576 Step=3, Dmax= 1.4e-01 nm, Epot= 1.56529e+08 Fmax= 2.20702e+09, atom= 11062 t = 0.004 ps: Water molecule starting at atom 16078 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=4, Dmax= 1.7e-01 nm, Epot= 2.11002e+10 Fmax= 5.75671e+13, atom= 14986 t = 0.005 ps: Water molecule starting at atom 14902 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=5, Dmax= 8.6e-02 nm, Epot= 1.22915e+07 Fmax= 4.57843e+07, atom= 6280 t = 0.006 ps: Water molecule starting at atom 15952 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=7, Dmax= 5.2e-02 nm, Epot= 5.50887e+06 Fmax= 1.19611e+08, atom= 7348 Step=8, Dmax= 6.2e-02 nm, Epot= 4.29974e+06 Fmax= 1.39548e+07, atom= 12066 Step=9, Dmax= 7.5e-02 nm, Epot= 1.93270e+06 Fmax= 2.81542e+07, atom= 7204 t = 0.010 ps: Water molecule starting at atom 7300 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 26, Dmax= 1.4e-06 nm, Epot= 2.53306e+06 Fmax= 8.74996e+06, atom= 15953 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1e-06 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 27 steps, but did not reach the requested Fmax < 1e-06. Potential Energy = 1.9327006e+06 Maximum force = 2.8154184e+07 on atom 7204 Norm of force = 4.1820662e+05 I checked the output .pdb files, and they show box is cracking from the position of the ice-water interface! Also, the ice part looks like a complete mess! (like it's not going to be ice anymore). I checked the .itp file to make sure are the variables are correct. Nothing looked wrong to me. I checked the mailing list about minimization. Just remember this water model is not flexible. Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 16, 2009 12:39 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > You were right! The dimensions of the box are zero in the .gro file. Should > I change them to the values I have? Set them using editconf Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] minimzation problem with a heterogeneous system
Dear Mark, I think I know the problem! I have simulated homogeneous systems (liquid water) without any problems. Problem is with the order of particles in the PDB or gro file which I use as my input. As the order of oxygen changes in the input, when I 'settle' the oxygen, then the corresponding Hs are not after my oxygen. So, settle takes sth else for constraining the system. Now, I need a smart advice on how to convert the order of particles in PDB or gro file in way that it matches the OHH format, not sth else. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, July 16, 2009 8:40 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] minimzation problem with a heterogeneous system Payman Pirzadeh wrote: > Hello, > I have a configuration in which half of the box is liquid water and the > other half is ice. This configuration is the output of another simulation in > which the mentioned config worked (and still works fine). But when I start > minimizing it (I started minimization since my first round of MD run crashed > due to messages indicative of clashes). But minimation ends with the > following message: > > Steepest Descents: >Tolerance (Fmax) = 1.0e-06 >Number of steps= 50 > Step=1, Dmax= 1.0e-01 nm, Epot= 6.09464e+11 Fmax= 1.31718e+14, atom= > 2938 > Step=2, Dmax= 1.2e-01 nm, Epot= 1.15027e+09 Fmax= 2.00242e+11, atom= > 2576 > Step=3, Dmax= 1.4e-01 nm, Epot= 1.56529e+08 Fmax= 2.20702e+09, atom= > 11062 > > t = 0.004 ps: Water molecule starting at atom 16078 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > Step=4, Dmax= 1.7e-01 nm, Epot= 2.11002e+10 Fmax= 5.75671e+13, atom= > 14986 > t = 0.005 ps: Water molecule starting at atom 14902 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > Step=5, Dmax= 8.6e-02 nm, Epot= 1.22915e+07 Fmax= 4.57843e+07, atom= > 6280 > > t = 0.006 ps: Water molecule starting at atom 15952 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > Step=7, Dmax= 5.2e-02 nm, Epot= 5.50887e+06 Fmax= 1.19611e+08, atom= > 7348 > Step=8, Dmax= 6.2e-02 nm, Epot= 4.29974e+06 Fmax= 1.39548e+07, atom= > 12066 > Step=9, Dmax= 7.5e-02 nm, Epot= 1.93270e+06 Fmax= 2.81542e+07, atom= > 7204 > > t = 0.010 ps: Water molecule starting at atom 7300 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > Step= 26, Dmax= 1.4e-06 nm, Epot= 2.53306e+06 Fmax= 8.74996e+06, atom= > 15953 > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1e-06 > > Double precision normally gives you higher accuracy. > You might need to increase your constraint accuracy, or turn > off constraints alltogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 27 steps, > but did not reach the requested Fmax < 1e-06. > Potential Energy = 1.9327006e+06 > Maximum force = 2.8154184e+07 on atom 7204 > Norm of force = 4.1820662e+05 > > I checked the output .pdb files, and they show box is cracking from the > position of the ice-water interface! Also, the ice part looks like a > complete mess! (like it's not going to be ice anymore). I checked the .itp > file to make sure are the variables are correct. Nothing looked wrong to me. > I checked the mailing list about minimization. Just remember this water > model is not flexible. All we can say is the something is broken with your model or initial configuration. Simplify it into small, homogeneous systems until you can diagnose the source of the problem. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] reliability of NOTES
Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:38 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > You were right! The dimensions of the box are zero in the .gro file. Should > I change them to the values I have? > As long as those vectors define the box size and not necessarily the system size (i.e., largest coordinate - smallest coordinate). You can do this with a .pdb file, I think on the CRYST line, if you prefer. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 16, 2009 12:08 PM > To: Gromacs Users' List > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> But, I am using a .pdb file as the input of the gromacs. Does the >> preparation of pdb file differ from software to software? >> > > It shouldn't, and I'm not 100% sure on how Gromacs handles system size from > a > .pdb file (I always use .gro). What you can try to do is transform your > .pdb > into .gro format with editconf, and read the last line of the .gro file. > That's > any easy way to determine the size of the box Gromacs is finding. > > -Justin > >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 16, 2009 11:42 AM >> To: Gromacs Users' List >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> Hello, >>> Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the >>> rvdw cutoff to 10A, but problem was still there. >>> Now I made my box bigger by using a visualization software. The new >>> dimensions are ~54*63*103.38(all in A). Again the same warning is given > to >>> me about increasing the box size or reduce the rvdw. >>> >> Well, Gromacs doesn't do anything in A, it's all nm, so be sure that >> everything >> you're doing is consistent with Gromacs conventions. There is no reason >> that >> either of those boxe should be complaining about a 1.0-nm cutoff, so there >> has >> to be something that messed up along the way. >> >> -Justin >> >>> Payman >>> >>> -Original Message- >>> From: gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] >>> On Behalf Of Justin A. Lemkul >>> Sent: July 15, 2009 7:32 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] making a box of water >>> >>> >>> >>> Payman Pirzadeh wrote: >>>> Hello, >>>> I have an .pdb file from another simulation. I want to make the >>> appropriate >>>> input files to run a simulations. I have used grompp to produce the .tpr >>>> file, but I get the usual ERROR: >>>> >>>> ERROR: The cut-off length is longer than half the shortest box vector > or >>>> longer than the smallest box diagonal element. Increase the box size or >>>> decrease rvdw. >>>> >>>> I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but > still >>>> the problem persists! Smaller rvdw is not good for my system. Any >>>> suggestions? >>>> >>> Then you'll have to use a bigger box, most likely. What is your smallest >>> box >>> vector? That should indicate the limits of your cutoffs. >>> >>> -Justin >>> >>>> Payman >>>> >>>> -Original Message- >>>> From: gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] >>>> On Behalf Of David van der Spoel >>>> Sent: July 15, 2009 12:23 PM >>>> To: Discussion list for GROMACS users >>>> Subject
[gmx-users] genconf
OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command "genconf". My original box has non-zero charge, but the generated bigger box has some charges: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using "genconf" that I am missing? Doesn't it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Vitaly V. Chaban Sent: July 21, 2009 4:53 PM To: gmx-users@gromacs.org Subject: [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute "berendsen" with "V-rescale" in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] genconf
In my previous e-mail, I posted the amount of charge given by GROMACS: > NOTE 2 [file sixsitemodel.top, line 8]: > > System has non-zero total charge: -1.220703e-04 Also, I run the system without multiplication, and it runs fine without any notes on the presence of a net charge!!! But, as soon as it is multiplied, then it gives notes of net charge! Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > OK! Thanks for the tips on thermostat. > > I multiplied my .gro file by using the command "genconf". My original > box has non-zero charge, but the generated bigger box has some charges: > > Define "non-zero." Is it at least an integer? Should your system bet net neutral at this stage in your system preparation? -Justin > > NOTE 2 [file sixsitemodel.top, line 8]: > > System has non-zero total charge: -1.220703e-04 > > > > Then, during minimization, the system experiences a large positive > potential and infinite force. Is there a technicality in using "genconf" > that I am missing? Doesn't it read the dimensions of the box from .gro > file to make sure no particles are overlapping with the original box? Or > no particle is coming from the new one in the old one? > > > > Payman > > > > *From:* gmx-users-boun...@gromacs.org > [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban > *Sent:* July 21, 2009 4:53 PM > *To:* gmx-users@gromacs.org > *Subject:* [gmx-users] Re: reliability of NOTES > > > > > Hello, > I am trying to prepare the input files for an MD run. After running > grompp, > I received the following note: > > NOTE 1 [file npt.mdp, line unknown]: > The Berendsen thermostat does not generate the correct kinetic energy > distribution. You might want to consider using the V-rescale > thermostat. > > How reliable this note is? > > > It's true. > > > And how can I implement V-rescale thermostat in y > input file (I found nothing in the manual). > > > Substitute "berendsen" with "V-rescale" in the mdp file. > > > Also, when I changed the thermostat to nose-hoover, it said that it > can not > be used with Berendsen barostat. Why? > > C'est la vie... > > > -- > Vitaly V. Chaban, Ph.D. (ABD) > School of Chemistry > V.N. Karazin Kharkiv National University > Svoboda sq.,4, Kharkiv 61077, Ukraine > email: cha...@univer.kharkov.ua > <mailto:cha...@univer.kharkov.ua>,vvcha...@gmail.com > <mailto:vvcha...@gmail.com> > skype: vvchaban, mob.: +38-097-8259698 > http://www-rmn.univer.kharkov.ua/chaban.html > === > !!! Looking for a postdoctoral position !!! > === > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] genconf
I am so sorry! I had sth in mind and I wrote sth else!!! My original box has zero charges and GROMACS shows no notes on this. As soon as the box is multiplies, then the note regarding the net charge shows up and causes the simulation to crash. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:25 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > In my previous e-mail, I posted the amount of charge given by GROMACS: > >> NOTE 2 [file sixsitemodel.top, line 8]: >> >> System has non-zero total charge: -1.220703e-04 > > Also, I run the system without multiplication, and it runs fine without any > notes on the presence of a net charge!!! But, as soon as it is multiplied, > then it gives notes of net charge! > Then I'm more confused (and hence why I asked the first time). You said your original system had a non-zero charge. Now you say that there were no notes about net charge, so the original system was uncharged. Depending on the size of your system, small rounding errors can accumulate and cause tiny fractional charges. I don't know if this is problematic or not (in terms of the system charge that mdrun finds), but it could be why you are seeing this note. -Justin > Payman > > > > > > > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 21, 2009 6:13 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] genconf > > > > Payman Pirzadeh wrote: >> OK! Thanks for the tips on thermostat. >> >> I multiplied my .gro file by using the command "genconf". My original >> box has non-zero charge, but the generated bigger box has some charges: >> >> > > Define "non-zero." Is it at least an integer? Should your system bet net > neutral at this stage in your system preparation? > > -Justin > >> NOTE 2 [file sixsitemodel.top, line 8]: >> >> System has non-zero total charge: -1.220703e-04 >> >> >> >> Then, during minimization, the system experiences a large positive >> potential and infinite force. Is there a technicality in using "genconf" >> that I am missing? Doesn't it read the dimensions of the box from .gro >> file to make sure no particles are overlapping with the original box? Or >> no particle is coming from the new one in the old one? >> >> >> >> Payman >> >> >> >> *From:* gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban >> *Sent:* July 21, 2009 4:53 PM >> *To:* gmx-users@gromacs.org >> *Subject:* [gmx-users] Re: reliability of NOTES >> >> >> >> >> Hello, >> I am trying to prepare the input files for an MD run. After running >> grompp, >> I received the following note: >> >> NOTE 1 [file npt.mdp, line unknown]: >> The Berendsen thermostat does not generate the correct kinetic energy >> distribution. You might want to consider using the V-rescale >> thermostat. >> >> How reliable this note is? >> >> >> It's true. >> >> >> And how can I implement V-rescale thermostat in y >> input file (I found nothing in the manual). >> >> >> Substitute "berendsen" with "V-rescale" in the mdp file. >> >> >> Also, when I changed the thermostat to nose-hoover, it said that it >> can not >> be used with Berendsen barostat. Why? >> >> C'est la vie... >> >> >> -- >> Vitaly V. Chaban, Ph.D. (ABD) >> School of Chemistry >> V.N. Karazin Kharkiv National University >> Svoboda sq.,4, Kharkiv 61077, Ukraine >> email: cha...@univer.kharkov.ua >> <mailto:cha...@univer.kharkov.ua>,vvcha...@gmail.com >> <mailto:vvcha...@gmail.com> >> skype: vvchaban, mob.: +38-097-8259698 >> http://www-rmn.univer.kharkov.ua/chaban.html >> === >> !!! Looking for a postdoctoral position !!! >> === >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.g
RE: [gmx-users] genconf
Yes and no! Sometimes there is an overlap, but sometimes I could find nothing! In the simplest case, how can we avoid overlaps in a way that the crystal structure is maintained under pbc? Can the option "-dist" help here? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > I am so sorry! I had sth in mind and I wrote sth else!!! > My original box has zero charges and GROMACS shows no notes on this. > As soon as the box is multiplies, then the note regarding the net charge > shows up and causes the simulation to crash. > Well, then, like I said, this is probably an accumulation of rounding errors. It can probably be ignored. The reason for the crash is more likely some kind of atomic overlap generated by the use of genconf. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: July 21, 2009 6:25 PM > To: Gromacs Users' List > Subject: Re: [gmx-users] genconf > > > > Payman Pirzadeh wrote: >> In my previous e-mail, I posted the amount of charge given by GROMACS: >> >>> NOTE 2 [file sixsitemodel.top, line 8]: >>> >>> System has non-zero total charge: -1.220703e-04 >> Also, I run the system without multiplication, and it runs fine without > any >> notes on the presence of a net charge!!! But, as soon as it is multiplied, >> then it gives notes of net charge! >> > > Then I'm more confused (and hence why I asked the first time). You said > your > original system had a non-zero charge. Now you say that there were no notes > > about net charge, so the original system was uncharged. > > Depending on the size of your system, small rounding errors can accumulate > and > cause tiny fractional charges. I don't know if this is problematic or not > (in > terms of the system charge that mdrun finds), but it could be why you are > seeing > this note. > > -Justin > >> Payman >> >> >> >> >> >> >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: July 21, 2009 6:13 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] genconf >> >> >> >> Payman Pirzadeh wrote: >>> OK! Thanks for the tips on thermostat. >>> >>> I multiplied my .gro file by using the command "genconf". My original >>> box has non-zero charge, but the generated bigger box has some charges: >>> >>> >> Define "non-zero." Is it at least an integer? Should your system bet net > >> neutral at this stage in your system preparation? >> >> -Justin >> >>> NOTE 2 [file sixsitemodel.top, line 8]: >>> >>> System has non-zero total charge: -1.220703e-04 >>> >>> >>> >>> Then, during minimization, the system experiences a large positive >>> potential and infinite force. Is there a technicality in using "genconf" >>> that I am missing? Doesn't it read the dimensions of the box from .gro >>> file to make sure no particles are overlapping with the original box? Or >>> no particle is coming from the new one in the old one? >>> >>> >>> >>> Payman >>> >>> >>> >>> *From:* gmx-users-boun...@gromacs.org >>> [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban >>> *Sent:* July 21, 2009 4:53 PM >>> *To:* gmx-users@gromacs.org >>> *Subject:* [gmx-users] Re: reliability of NOTES >>> >>> >>> >>> >>> Hello, >>> I am trying to prepare the input files for an MD run. After running >>> grompp, >>> I received the following note: >>> >>> NOTE 1 [file npt.mdp, line unknown]: >>> The Berendsen thermostat does not generate the correct kinetic > energy >>> distribution. You might want to consider using the V-rescale >>> thermostat. >>> >>> How reliable this note is? >>> >>> >>> It's true. >>> &g
RE: [gmx-users] genconf
Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 21, 2009 11:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > Yes and no! > Sometimes there is an overlap, but sometimes I could find nothing! In the > simplest case, how can we avoid overlaps in a way that the crystal structure > is maintained under pbc? > Can the option "-dist" help here? Replicating a box that was not designed for periodicity will always have this problem. Whether the box is too small or two large, there will either be steric clashes, or vacuums that will need filling. The general solution is to equilibrate your box under PBC prior to replication. Now the box size and the atomic spacings will be plausible, and the replication will not of necessity introduce artifacts. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] genconf
Hello, I minimized the initial output (from another simulation) first; then I replicated it. This time, the minimization of the bigger box was done more easily! I ran an MD simulation with the bigger box and after 6 hours, it has not crashed yet. But, I have a question. When we replicate a box, and in the primary box one molecule is dissected into pieces due to pbc, will GROMACS return the molecules to its original shape during MD run or not? I believe, without minimization, these dissected pieces will remain in the middle of the box and interfere with their replicated versions. Maybe, 'genconf' should be modified for such replications to maintain the pbc between the new molecules at the boundaries and fix the problem with the particle in the middle of the new bigger box! Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 22, 2009 9:22 AM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] genconf Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 21, 2009 11:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > Yes and no! > Sometimes there is an overlap, but sometimes I could find nothing! In the > simplest case, how can we avoid overlaps in a way that the crystal structure > is maintained under pbc? > Can the option "-dist" help here? Replicating a box that was not designed for periodicity will always have this problem. Whether the box is too small or two large, there will either be steric clashes, or vacuums that will need filling. The general solution is to equilibrate your box under PBC prior to replication. Now the box size and the atomic spacings will be plausible, and the replication will not of necessity introduce artifacts. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] genconf
Hi Justin, I checked the trjconv help. It also takes .gro files. If so, do I still need to provide a .tpr file? (if yes, then the output can be .gro?) Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 22, 2009 6:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > Hello, > I minimized the initial output (from another simulation) first; then I > replicated it. This time, the minimization of the bigger box was done more > easily! I ran an MD simulation with the bigger box and after 6 hours, it has > not crashed yet. > But, I have a question. When we replicate a box, and in the primary box one > molecule is dissected into pieces due to pbc, will GROMACS return the > molecules to its original shape during MD run or not? No, it does not. > I believe, without minimization, these dissected pieces will remain in the > middle of the box and interfere with their replicated versions. Maybe, > 'genconf' should be modified for such replications to maintain the pbc > between the new molecules at the boundaries and fix the problem with the > particle in the middle of the new bigger box! > It can easily be accomplished using a .tpr file, and by using trjconv -pbc whole. After molecules are whole, then use genconf. -Justin > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Payman Pirzadeh > Sent: July 22, 2009 9:22 AM > To: 'Discussion list for GROMACS users' > Subject: RE: [gmx-users] genconf > > Thanks a lot Mark! I will run the system for equilibration and then try to > replicate it. I will keep you guys posted. > > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Mark Abraham > Sent: July 21, 2009 11:01 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] genconf > > Payman Pirzadeh wrote: >> Yes and no! >> Sometimes there is an overlap, but sometimes I could find nothing! In the >> simplest case, how can we avoid overlaps in a way that the crystal > structure >> is maintained under pbc? >> Can the option "-dist" help here? > > Replicating a box that was not designed for periodicity will always have > this problem. Whether the box is too small or two large, there will > either be steric clashes, or vacuums that will need filling. The general > solution is to equilibrate your box under PBC prior to replication. Now > the box size and the atomic spacings will be plausible, and the > replication will not of necessity introduce artifacts. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Rea
RE: [gmx-users] Re: wierd behavior of mdrun
There is sth strange about this problem which I suspect it might be due to the mdp file and input. I can run the energy minimization without any problems (I submit the job and it apparently works using the same submission script)! But as soon as I prepare the tpr file for MD run, then I run into this run-without-output trouble. Again I paste my mdp file below (I want to run an NVT run): cpp = cpp include = -I../top define = -DPOSRES ; Run control integrator = md dt = 0.001 ;1 fs nsteps = 300 ;3 ns comm_mode= linear nstcomm = 1 ;Output control nstxout = 5000 nstlog = 5000 nstenergy= 5000 nstxtcout= 1500 nstvout = 5000 nstfout = 5000 xtc_grps = energygrps = ; Neighbour Searching nstlist = 10 ns_type = grid rlist= 0.9 pbc = xyz ; Electrostatistics coulombtype = PME rcoulomb = 0.9 ;epsilon_r= 1 ; Vdw vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres ;Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 optimize_fft= yes ; Temperature coupling tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t= 0.1 ref_t= 275 ; Pressure Coupling Pcoupl = no ;Pcoupltype = isotropic ;tau_p= 1.0 ;compressibility = 5.5e-5 ;ref_p= 1.0 gen_vel = yes gen_temp = 275 gen_seed = 173529 constraint-algorithm = Lincs constraints = all-bonds lincs-order = 4 Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: August 27, 2009 3:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: wierd behavior of mdrun Vitaly V. Chaban wrote: > Then I believe you have problems with MPI. > > Before I experienced something alike on our old system - serial > version worked OK but parallel one failed. The same issue was with > CPMD by the way. Another programs worked fine. I didn't correct that > problem... > > On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadeh wrote: >> Yes, >> it works when it is run on one processor interactively! That's fine, but it doesn't mean the problem is with the parallelism, as Vitaly suggests. If your cluster filesystem isn't configured properly, you will observe these symptoms. Since the submission script was the same, MPI worked previously, so isn't likely to be the problem... Mark >> On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote: I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is running, also the processors are 100% engaged while I have no outputs! >>> A standard guess: what about trying to run the single-processor job on >>> the same cluster? Does it run OK? >>> >>> > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: {Spam?} Re: [gmx-users] Re: wierd behavior of mdrun
I have checked my job on another cluster which is dual core. On one node, it
just ran fine! I think sth might be wrong with the cluster settings. I will
try the output settings you suggested as well. I will keep you posted.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Friday, September 04, 2009 5:29 PM
To: Gromacs Users' List
Subject: {Spam?} Re: [gmx-users] Re: wierd behavior of mdrun
Have you tried my suggestion from the last message of setting frequent
output?
Could your system just be collapsing at the outset of the simulation?
Setting
nstxout = 1 would catch something like this.
There is nothing special about treating a protein in parallel vs. a system
of
water. Since a system of water runs just fine, it seems even more likely to
me
that your system is simply crashing immediately, rather than a problem with
Gromacs or the MPI implementation.
-Justin
Paymon Pirzadeh wrote:
> Regarding the problems I have on running protein system in parallel
> (runs without output), When I run pure water system, everything is fine,
> I have tested pure water systems 8 times larger than my protein system.
> while the former runs fine, the latter has problems. I have also tested
> pure water systems with approximately same number of sites in .gro file
> as in my protein .gro file, and with the same input file in terms of
> spitting outputs; they are fine.I would like to know what happens to
> GROMACS when a protein is added to the system. The cluster admin has not
> get back to me, but I still want to check there is no problem with my
> setup! (although my system runs fine in serial mode).
> Regards,
>
> Payman
>
>
>
> On Fri, 2009-08-28 at 16:41 -0400, Justin A. Lemkul wrote:
>> Payman Pirzadeh wrote:
>>> There is sth strange about this problem which I suspect it might be due
to
>>> the mdp file and input. I can run the energy minimization without any
>>> problems (I submit the job and it apparently works using the same
submission
>>> script)! But as soon as I prepare the tpr file for MD run, then I run
into
>>> this run-without-output trouble.
>>> Again I paste my mdp file below (I want to run an NVT run):
>>>
>> There isn't anything in the .mdp file that suggests you wouldn't get any
output.
>> The output of mdrun is buffered, so depending on your settings, you may
have
>> more frequent output during energy minimization. There may be some
problem with
>> the MPI implementation in buffering and communicating data properly.
That's a
>> bit of a guess, but it could be happening.
>>
>> Definitely check with the cluster admin to see if there are any error
messages
>> reported for the jobs you submitted.
>>
>> Another test you could do to force a huge amount of data would be to set
all of
>> your outputs (nstxout, nstxtcout, etc) = 1 and run a much shorter
simulation (to
>> prevent massive data output!); this would force more continuous data
through the
>> buffer.
>>
>> -Justin
>>
>>> cpp = cpp
>>> include = -I../top
>>> define = -DPOSRES
>>>
>>> ; Run control
>>>
>>> integrator = md
>>> dt = 0.001 ;1 fs
>>> nsteps = 300 ;3 ns
>>> comm_mode= linear
>>> nstcomm = 1
>>>
>>> ;Output control
>>>
>>> nstxout = 5000
>>> nstlog = 5000
>>> nstenergy= 5000
>>> nstxtcout= 1500
>>> nstvout = 5000
>>> nstfout = 5000
>>> xtc_grps =
>>> energygrps =
>>>
>>> ; Neighbour Searching
>>>
>>> nstlist = 10
>>> ns_type = grid
>>> rlist= 0.9
>>> pbc = xyz
>>>
>>> ; Electrostatistics
>>>
>>> coulombtype = PME
>>> rcoulomb = 0.9
>>> ;epsilon_r= 1
>>>
>>> ; Vdw
>>>
>>> vdwtype = cut-off
>>> rvdw = 1.2
>>> DispCorr = EnerPres
>>>
>>> ;Ewald
>>>
>>> fourierspacing = 0.12
>>> pme_order = 4
>>> ewald_rtol = 1e-6
>>> optimize_fft= yes
>>>
>>> ; Temperature coupling
>>>
>>> tcoupl = v-rescale
>>> ld_seed = -1
>>> tc-grps = System
>>> tau_t= 0.1
>>> ref_t= 275
>>>
>&g
[gmx-users] a naive question on restraints and constraints
Hi, I read the wiki and manual on constraint and restraints, and I am still a bit confused. But, my question is, should I remove the restraints after equilibration in production phase? What about constraints? How should I know my system really needs either of them (is there a general rule or protocol to follow)? If I apply them incorrectly, how will them affect my results (in my case protein)? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 17, 2009 5:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] merging simulation boxes Paymon Pirzadeh wrote: > I have a box of crystal (from another simulation) and a box of solvated > protein. Now I want to put the protein close to my crystal. > Use editconf to define a box for your new system, use -center on each component as appropriate, and cat the two .gro files together (removing the duplicate box info, etc that will be placed in the middle of the new file). -Justin > Payman > > > > > On Fri, 2009-09-18 at 09:04 +1000, Mark Abraham wrote: >> Paymon Pirzadeh wrote: >>> Hello, >>> Are there any links on how we can merge two simulation boxes to make a >>> single configuration? What technicalities should be considered? >> Define "merge". There's a whole pile of issues depending what you mean. >> >> Why can't you build initial coordinates up from scratch, rather than >> "merge" some pre-existing sets? >> >> Mark >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] viscosity calculation
Hello, I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Regards, Payman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation
Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. 2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: > Hello, > > I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity > of my system which is water. Two files are generate: *.xvg and the > enecorr.xvg. Now, what should I do to calculate the viscosity of my > system with these two files? Sorry for such naïve question. > Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin > > > Regards, > > > > Payman > > > > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation
Apparently, in the file the unit in the file is cP. It might be the case that I plotted the wrong column. I think I should get the third column. Regarding the diffusion, I read in papers about rotational diffusion of the proteins which could be calculated having the viscosity of the liquid and hydrodynamic volume of the protein. So, volume could be calculated with radius of gyration + 0.3nm of hydration shell and viscosity is given by g_energy. So, a rotational diffusion constant could be theoretically calculated. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: > Well, two questions: > > 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like > very weird to me since experimental value for water viscosity is 0.854 cP. > My system is at 265K with 4202 molecules. Is sth strange going on? Or I am > missing some unit conversions in the plot. > Is the experimental value 0.854 at that temperature? Could be the the unit is different in the output too. Doesn't it say in the xvg file? > 2. For calculation of protein diffusion constant, should we use the bulk or > shear viscosity of the solvent (water)? Why not use g_msd? > > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: September 29, 2010 12:28 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] viscosity calculation > > > > Payman Pirzadeh wrote: >> Hello, >> >> I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity >> of my system which is water. Two files are generate: *.xvg and the >> enecorr.xvg. Now, what should I do to calculate the viscosity of my >> system with these two files? Sorry for such naïve question. >> > > Plot the output .xvg; you will find it should contain two quantities: bulk > and > shear viscosity. > > -Justin > >> >> >> Regards, >> >> >> >> Payman >> >> >> >> >> > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation_2
Adding to my previous comments, It looks like that the third column is the appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to take the whole trajectory (2 ps) rather than half of the frames. But, still g_energy take half of the frames. This has caused improper convergence in viscosity values. If I take only the last 3000 ps (out of 1ps), I will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy switches? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: > Well, two questions: > > 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like > very weird to me since experimental value for water viscosity is 0.854 cP. > My system is at 265K with 4202 molecules. Is sth strange going on? Or I am > missing some unit conversions in the plot. > Is the experimental value 0.854 at that temperature? Could be the the unit is different in the output too. Doesn't it say in the xvg file? > 2. For calculation of protein diffusion constant, should we use the bulk or > shear viscosity of the solvent (water)? Why not use g_msd? > > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Justin A. Lemkul > Sent: September 29, 2010 12:28 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] viscosity calculation > > > > Payman Pirzadeh wrote: >> Hello, >> >> I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity >> of my system which is water. Two files are generate: *.xvg and the >> enecorr.xvg. Now, what should I do to calculate the viscosity of my >> system with these two files? Sorry for such naïve question. >> > > Plot the output .xvg; you will find it should contain two quantities: bulk > and > shear viscosity. > > -Justin > >> >> >> Regards, >> >> >> >> Payman >> >> >> >> >> > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation_2
Thanks for the tips. I just realized that there two other outputs two the g_energy -vis: evisco.xvg and eviscoi.xvg These files contain 5 columns among which the first one looks to be time. But what are the other 4? What are their differences? Regards, Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 2:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation_2 On 2010-09-29 22.00, Payman Pirzadeh wrote: > Adding to my previous comments, It looks like that the third column is the > appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to > take the whole trajectory (2 ps) rather than half of the frames. But, > still g_energy take half of the frames. This has caused improper convergence > in viscosity values. If I take only the last 3000 ps (out of 1ps), I > will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy > switches? > I think this is because it use an autocorrelation function of the pressure. By default it uses an FFT to compute it. The ACF at 2 ps has very poor statistics (1 data point) and can therefore ruin the viscosity. Therefore ACFs by default are plotted to half the traj. There is a flag to get a longer (noisier) ACF. g_energy -h might tell you which one. > Payman > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of David van der Spoel > Sent: September 29, 2010 1:03 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] viscosity calculation > > On 2010-09-29 20.52, Payman Pirzadeh wrote: >> Well, two questions: >> >> 1. My bulk values are fluctuating around 60 (I assume cP). But it looks > like >> very weird to me since experimental value for water viscosity is 0.854 cP. >> My system is at 265K with 4202 molecules. Is sth strange going on? Or I am >> missing some unit conversions in the plot. >> > Is the experimental value 0.854 at that temperature? > Could be the the unit is different in the output too. Doesn't it say in > the xvg file? > >> 2. For calculation of protein diffusion constant, should we use the bulk > or >> shear viscosity of the solvent (water)? > Why not use g_msd? > >> >> Payman >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: September 29, 2010 12:28 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] viscosity calculation >> >> >> >> Payman Pirzadeh wrote: >>> Hello, >>> >>> I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity >>> of my system which is water. Two files are generate: *.xvg and the >>> enecorr.xvg. Now, what should I do to calculate the viscosity of my >>> system with these two files? Sorry for such naïve question. >>> >> >> Plot the output .xvg; you will find it should contain two quantities: bulk >> and >> shear viscosity. >> >> -Justin >> >>> >>> >>> Regards, >>> >>> >>> >>> Payman >>> >>> >>> >>> >>> >> > > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation_2
It does not explain for all files or all columns. For example, in the evisco.xvg, the following lines are written, but there are 5 columns (one of which is time). What are the rest? And the unit of the column (written below) is not clear to me. @title "Shear viscosity using Einstein relation" @xaxis label "Time (ps)" @yaxis label "(kg m\S-1\N s\S-1\N)" Same column are in the eviscoi.xvg (below). @title "Shear viscosity integral" @xaxis label "Time (ps)" @yaxis label "(kg m\S-1\N s\S-1\N ps)" I do not exactly know the relation between the two files and how I should use them. Also, the enecorr.xvg looks like to be a correlation function. But its unit is not clear and I do not know how to use it. I will be appreciated if you could clarify them. Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Dallas Warren Sent: September 29, 2010 7:11 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] viscosity calculation_2 Sorry, haven't looked at these files before so this might not be the case, but doesn't the top of the .xvg file explain what each column is? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_principal outputs
Hello, When we calculate the principal axes of protein, for each axis file, there are 4 columns. The first one is the time (ps), but there are no descriptions in the files about the rest. A little explanation will be very helpful. Regards, Payman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] editconf
After rotation, wouldn't a minimization with very very small steps solve the problem? Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: October 18, 2010 7:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote: > Hello, > I am trying to rotate my protein in my simulation box (solvent molecules > are there as well). I issue the following command: > editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15 > 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328 > > I select my group (protein) in the first group selection prompt and > whole system as output in the second prompt. However, in the output file > the whole system is rotated rather than protein only. Also, despite the > -box switch used, the dimensions of the box changes. > Is there any ideas on what I am missing in my procedure? editconf can't rotate the solute with solvent present - what would you like it to do about the voids and clashes that would be created? Do your rotation before you solvate. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] editconf
Dear Mark and Justin, Thanks for very informative comments. I'll try to rotate and then solvate. Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: October 18, 2010 7:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf On 19/10/2010 12:22 PM, Payman Pirzadeh wrote: > After rotation, wouldn't a minimization with very very small steps solve the > problem? Only if the solute surface was very close to being symmetric about the rotation axis. Since that never happens, editconf doesn't even have the ability to try. Mark > Paymon > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Mark Abraham > Sent: October 18, 2010 7:14 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] editconf > >On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote: >> Hello, >> I am trying to rotate my protein in my simulation box (solvent molecules >> are there as well). I issue the following command: >>editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15 >> 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328 >> >> I select my group (protein) in the first group selection prompt and >> whole system as output in the second prompt. However, in the output file >> the whole system is rotated rather than protein only. Also, despite the >> -box switch used, the dimensions of the box changes. >> Is there any ideas on what I am missing in my procedure? > editconf can't rotate the solute with solvent present - what would you > like it to do about the voids and clashes that would be created? Do your > rotation before you solvate. > > Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] viscosity calculations
Hello, I am trying to calculate the viscosity of my pure water system at 275K. The system has run for 40ns. I issued the following command: g_energy_d_mpi -f 275K_50_50_50_2.edr -s 275K_50_50_50_2.tpr -nmol 4202 -vis sixsitewater_275K -b 0 -e 4 The numbers I get in the output file are almost 100 times bigger than reported literature. Am I doing something wrong or in the analysis procedure sth is not divided properly? Also, I tried to calculate the viscosity through the transverse current autocorrelation function. The command I issued was: g_tcaf_d_mpi -f 275K_50_50_50_2.trr -s 275K_50_50_50_2.tpr -oc 275K_50_50_50_2 -ov 275K_50_50_50_2 -mol -wt 5 -n watermolecules.ndx The output is: k 1.253 tau 2.383 eta 0.14641 10^-3 kg/(m s) irow = 2, icol = 2 2225392908111942225202360202531386163200.000 -0.195 0.195 0.000 Numerical Recipes run-time error... GAUSSJ: Singular Matrix-2 Fit failed! k 1.253 tau 1.000 eta 0.15845 10^-3 kg/(m s) k 1.253 tau 0.133 eta 0.44011 10^-3 kg/(m s) k 1.771 tau 0.455 eta 0.10514 10^-3 kg/(m s) k 1.771 tau 1.458 eta 0.08329 10^-3 kg/(m s) k 1.771 tau 0.348 eta 0.13366 10^-3 kg/(m s) k 1.771 tau 0.324 eta 0.27031 10^-3 kg/(m s) k 1.771 tau 0.320 eta 0.14002 10^-3 kg/(m s) k 1.771 tau 2.100 eta 0.07649 10^-3 kg/(m s) k 2.169 tau 1.541 eta 0.05321 10^-3 kg/(m s) k 2.169 tau 2.201 eta 0.04949 10^-3 kg/(m s) irow = 1, icol = 1 0.000 -0.126 0.126 708363867825344.750 Numerical Recipes run-time error... GAUSSJ: Singular Matrix-2 Fit failed! k 2.169 tau 1.000 eta 0.05282 10^-3 kg/(m s) k 2.169 tau 0.997 eta 0.07365 10^-3 kg/(m s) k 2.505 tau 0.511 eta 0.05450 10^-3 kg/(m s) irow = 1, icol = 1 0.000 0.710 -0.710 34533840121856978944.000 Numerical Recipes run-time error... GAUSSJ: Singular Matrix-2 Fit failed! k 2.505 tau 1.000 eta 0.03961 10^-3 kg/(m s) k 2.505 tau 0.248 eta 0.06944 10^-3 kg/(m s) Averaged over k-vectors: k 1.253 tau 0.529 Omega 1.189 eta 0.35612 10^-3 kg/(m s) k 1.771 tau 0.458 Omega 0.832 eta 0.14388 10^-3 kg/(m s) k 2.169 tau 1.540 Omega 1.601 eta 0.05491 10^-3 kg/(m s) k 2.505 tau 0.280 Omega 0.499 eta 0.07050 10^-3 kg/(m s) I do not understand the failure parts of the output, also what should I do with the output numbers? I took a look at the -ov output. The final 4 numbers are not fittable on a eta(k)=eta(0)*(1-ak^2). Am I fitting the wrong data? Sorry for such a huge e-mail. Paymon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users]site-site radial distribution function
Hello, I have two questions about using g_rdf: 1. Is it meaningful to calculate the radial distribution of water molecules around a single atom of a surface residue, e.g. dangling OG1 oxygen of Threonine? (Does g_rdf takes care of the protein presence and the excluded volume?) 2. How will the RDF be calculated in a heterogeneous system? For instance, if you have protein in a solvent near a solvent's crystal's surface? What is considered as the bulk density of the solvent? Whole box? Thanks. Paymon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] trjcat xtc files
Your second guess is correct! I used grompp to restart (I had thought it might provide me with the chance to change things if needed). I was surprised initially when "cat" command did not work! The number of frames were most of the time less than what it should be. I also checked the 'trjcat -h'. I did not specifically understand how I might be able to get over this issue. Any advices? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Sunday, November 01, 2009 8:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] trjcat xtc files Paymon Pirzadeh wrote: > Sorry, > My command line was: > > trjcat_d_mpi -f AFPI_Ih1010_54_58_Npt265_2.xtc > AFPI_Ih1010_54_58_Npt265_3.xtc AFPI_Ih1010_54_58_Npt265_4.xtc > AFPI_Ih1010_54_58_Npt265_5.xtc AFPI_Ih1010_54_58_Npt265_6.xtc -o > AFPI_Ih1010_54_58_Npt265_merged2-6.xtc > > the "_d_mpi" is the suffix used for double precision and parallel > version of the installed gromacs. OK so now we have some idea what you might be trying to do. The most likely causes are that the first few trajectories have no frames, or that each frame in the earlier trajectories is common to one in the last trajectory. This might happen if you were using grompp to do restarts, or have previously assigned duplicate times somehow. If so, find a better workflow in future. Consult trjcat -h for clues on how to get around this. Mark > Payman > > On Mon, 2009-11-02 at 15:08 +1100, Mark Abraham wrote: >> Paymon Pirzadeh wrote: >>> Hello, >>> I am trying to concatenate several xtc files. When I use the trjcat, it >>> only writes the last file into the output file! where the problem could >>> be? >> In your command line. Why didn't you tell us what it was? :-) >> >> Mark >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] extracting individual particles properties
Hello, This is the third time I am sending this e-mail, and I am not sure why it does not show up on the list I have a simulation from which I have the .edr, .xtc and .trr files. I want to color my particles based on rmsd, potential energy, Sg (tetrahedral parameter) or any other parameters in a specific configuration. Is there a way to extract individual particle's properties out of these files? Thanks. Payman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
