[gmx-users] grompp error no. of coordinate file doesn't match with topology file
Dear all I am doing simulation of membrane protein ,for this first i did the concatanation of protein in lipid bilayer in proper orientation after that I am using inflategro script of teleman sir but after doing first step successfully I am getting problem in second step i,e energy minimisation step. problem is related with coordinate file which I putted with grompp and my topology file which I have made like this- Include forcefield parameters #include "ffG53a6_lipid.itp" ; Include DMPC chain topology #include "dmpc.itp" ; Include protein chain topologies #include "tap-mod.itp" #ifdef POSRES_PROTEIN #include "tap-mod_pr.itp" #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in DMPC bilayer [ molecules ] ; Namenumber Protein_X 1 DMPC 119 NA+ 1 And the problem I am getting like this-- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 770 of the 2278 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_X' Excluding 3 bonded neighbours molecule type 'DMPC' Excluding 1 bonded neighbours molecule type 'NA+' processing coordinates... --- Program grompp, VERSION 4.0.3 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (inflated_dmpc.gro, 13253) does not match topology (inflated_dmpc.top, 15392) --- If anyone have idea about this problem please suggest me something to solve this problem. Thnks a lot in advance. Nitu Sharma School of life sciences. Jawaherlal Nehru University New Delhi , India ___ 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] grompp error no. of coordinate file doesn't match with topology file
Dear all I am doing simulation of membrane protein ,for this first i did the concatanation of protein in lipid bilayer in proper orientation after that I am using inflategro script of teleman sir but after doing first step successfully I am getting problem in second step i,e energy minimisation step. problem is related with coordinate file which I putted with grompp and my topology file which I have made like this- Include forcefield parameters #include "ffG53a6_lipid.itp" ; Include DMPC chain topology #include "dmpc.itp" ; Include protein chain topologies #include "tap-mod.itp" #ifdef POSRES_PROTEIN #include "tap-mod_pr.itp" #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in DMPC bilayer [ molecules ] ; Namenumber Protein_X 1 DMPC 119 NA+ 1 And the problem I am getting like this-- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 770 of the 2278 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_X' Excluding 3 bonded neighbours molecule type 'DMPC' Excluding 1 bonded neighbours molecule type 'NA+' processing coordinates... --- Program grompp, VERSION 4.0.3 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (inflated_dmpc.gro, 13253) does not match topology (inflated_dmpc.top, 15392) --- If anyone have idea about this problem please suggest me something to solve this problem. Thnks a lot in advance. Nitu Sharma School of life sciences. Jawaherlal Nehru University New Delhi , India ___ 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] Problem with grompp?
Hi Bram, Check the creation times for topol.tpr and minimized.gro. First test the assumption that the former was created later than the latter. If it's not, then check the grompp output for errors. Maybe pasting it here can help. Cheers, Tsjerk On Thu, Apr 16, 2009 at 10:57 AM, Hoof, B. van wrote: > Hi Justin, > > Thanks for your answer. I am afraid, however, that the problem is then > somewhat different. Using > grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 > should have created a new topol.tpr, should it not? It did so in previous > times at least. > > If someone knows where I am going wrong, please let me know. > > Kind regards, > Bram > > > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On > Behalf Of Justin A. Lemkul > Sent: woensdag 15 april 2009 18:12 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Problem with grompp? > > > > Hoof, B. van wrote: >> Hi everyone, >> >> Since I am a new user of Gromacs, this problem is probably rather trivial, >> but I hope one of you would like to help me nonetheless. I have created a >> starting structure in a not very optimal situation, which I have then >> minimized. To continue, I would like to equilibrate the system further using >> leap-frog MD. To do so, I have used grompp in the following way: >> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 >> >> This creates the following mdout.mdp: see attachment >> >> Now as far as I can see, using the command `mdrun -v -c md_run.gro' should >> result in performing a 1,000,000 iteration md simulation of this system. >> However, when I issue that command, instead what I get is this: >> :-) G R O M A C S (-: >> >> Good ROcking Metal Altar for Chronical Sinners >> >> :-) VERSION 4.0.4 (-: >> >> >> [...] >> >> :-) mdrun (-: >> >> Option Filename Type Description >> >> [...] >> >> Getting Loaded... >> Reading file topol.tpr, VERSION 4.0.4 (single precision) >> Loaded with Money >> >> Steepest Descents: >> Tolerance (Fmax) = 1.0e+01 >> Number of steps = 1 >> Step= 1, Dmax= 1.0e-02 nm, Epot= 1.23314e+20 Fmax= 2.04950e+19, atom= >> 11163 >> Step= 2, Dmax= 1.2e-02 nm, Epot= 5.22616e+17 Fmax= 2.22256e+20, atom= >> 10863 >> Step= 3, Dmax= 1.4e-02 nm, Epot= 1.46382e+17 Fmax= 7.52962e+17, atom= >> 10593 >> Step= 4, Dmax= 1.7e-02 nm, Epot= 1.21703e+17 Fmax= 3.72098e+16, atom= >> 10331 >> Step= 5, Dmax= 2.1e-02 nm, Epot= 2.22862e+16 Fmax= 4.87326e+18, atom= >> 10857 >> Step= 6, Dmax= 2.5e-02 nm, Epot= 1.09032e+16 Fmax= 4.39937e+15, atom= >> 15106 >> Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81517e+15 Fmax= 6.07049e+14, atom= >> 15230 >> Step= 8, Dmax= 3.6e-02 nm, Epot= 2.84750e+14 Fmax= 9.82848e+14, atom= >> 14675 >> Step= 9, Dmax= 4.3e-02 nm, Epot= 2.33131e+14 Fmax= 2.39469e+13, atom= >> 11419 >> Step= 10, Dmax= 5.2e-02 nm, Epot= 7.23189e+12 Fmax= 2.72305e+14, atom= >> 14565 >> Step= 11, Dmax= 6.2e-02 nm, Epot= 3.19510e+12 Fmax= 4.82192e+12, atom= >> 10638 >> Step= 13, Dmax= 3.7e-02 nm, Epot= 1.82616e+12 Fmax= 1.11184e+13, atom= >> 11929 >> [... etc.] >> <<< >> >> This is a minimization using the steepest descent algorithm. What am I doing >> wrong here? >> >> Thank you in advance for your kind help! >> > > If you use default names (i.e., topol.tpr for output), you can easily confuse > yourself and wind up running the wrong input file. The mdout.mdp file you > posted should correspond to MD; most likely you've just re-run the same .tpr > file that you used for minimization. > > -Justin > >> Greetings, >> Bram van Hoof >> >> >> >> >> >> >> >> >> ___ >> 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 > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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 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 lis
Re: [gmx-users] grompp error no. of coordinate file doesn't match with topology file
nitu sharma wrote: Dear all I am doing simulation of membrane protein ,for this first i did the concatanation of protein in lipid bilayer in proper orientation after that I am using inflategro script of teleman sir but after doing first step successfully I am getting problem in second step i,e energy minimisation step. problem is related with coordinate file which I putted with grompp and my topology file which I have made like this- Include forcefield parameters #include "ffG53a6_lipid.itp" ; Include DMPC chain topology #include "dmpc.itp" ; Include protein chain topologies #include "tap-mod.itp" #ifdef POSRES_PROTEIN #include "tap-mod_pr.itp" #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in DMPC bilayer [ molecules ] ; Namenumber Protein_X 1 DMPC 119 NA+ 1 And the problem I am getting like this-- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 770 of the 2278 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_X' Excluding 3 bonded neighbours molecule type 'DMPC' Excluding 1 bonded neighbours molecule type 'NA+' processing coordinates... --- Program grompp, VERSION 4.0.3 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (inflated_dmpc.gro, 13253) does not match topology (inflated_dmpc.top, 15392) --- The only way to answer this question is to look in the coordinate file, look in the topology (not what you keep posting, but the actual .itp file(s) for your protein, etc). There are several possible problems, but these are all just guesses on my part: 1. You did the concatenation wrong, and you have duplicates of many of your species. 119 DMPC lipids should correspond to 5474 atoms under a UA representation. Is your protein really 10,000 atoms? 2. Why do you have NA+ present? InflateGRO should have stripped out everything that was not protein or lipid. Even if it didn't, you don't need to add ions yet. 3. Do you have [ molecules ] sections in your .itp files? This can lead to duplication in the topology. -Justin If anyone have idea about this problem please suggest me something to solve this problem. Thnks a lot in advance. Nitu Sharma School of life sciences. Jawaherlal Nehru University New Delhi , India ___ 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 Graduate Research Assistant 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
Re: [gmx-users] Problem with grompp?
Hi Bram, So to echo Justin, it's really better if you use distinct names for the files generated at each step. The -deffnm option to mdrun can be helpful there too. This will help you avoid mistakes like this _and_ will ensure you have all the files available in case you need to check where things went wrong if they do. Cheers, Tsjerk On Thu, Apr 16, 2009 at 12:37 PM, Hoof, B. van wrote: > Yes, indeed. The file topol.tpr was not re-created when I used grompp. In > fact, an error was thrown by grompp stating file input/output error: > minimized.gro > > I am embarrased to say that I had used the command >> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -o membr.tpr >> -maxwarn 10 > instead of >> grompp -f martini_md1.mdp -c minimised.gro -p martini.top -o membr.tpr >> -maxwarn 10 > > Unfortunately, because mdout.mdp was created correctly, I hadn't noticed this > error. > > Thank you everyone for your help! > Bram van Hoof > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On > Behalf Of Tsjerk Wassenaar > Sent: donderdag 16 april 2009 12:11 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Problem with grompp? > > Hi Bram, > > Check the creation times for topol.tpr and minimized.gro. First test > the assumption that the former was created later than the latter. If > it's not, then check the grompp output for errors. Maybe pasting it > here can help. > > Cheers, > > Tsjerk > > On Thu, Apr 16, 2009 at 10:57 AM, Hoof, B. van wrote: >> Hi Justin, >> >> Thanks for your answer. I am afraid, however, that the problem is then >> somewhat different. Using >> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 >> should have created a new topol.tpr, should it not? It did so in previous >> times at least. >> >> If someone knows where I am going wrong, please let me know. >> >> Kind regards, >> Bram >> >> >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: woensdag 15 april 2009 18:12 >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Problem with grompp? >> >> >> >> Hoof, B. van wrote: >>> Hi everyone, >>> >>> Since I am a new user of Gromacs, this problem is probably rather trivial, >>> but I hope one of you would like to help me nonetheless. I have created a >>> starting structure in a not very optimal situation, which I have then >>> minimized. To continue, I would like to equilibrate the system further >>> using leap-frog MD. To do so, I have used grompp in the following way: >>> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 >>> >>> This creates the following mdout.mdp: see attachment >>> >>> Now as far as I can see, using the command `mdrun -v -c md_run.gro' should >>> result in performing a 1,000,000 iteration md simulation of this system. >>> However, when I issue that command, instead what I get is this: >>> :-) G R O M A C S (-: >>> >>> Good ROcking Metal Altar for Chronical Sinners >>> >>> :-) VERSION 4.0.4 (-: >>> >>> >>> [...] >>> >>> :-) mdrun (-: >>> >>> Option Filename Type Description >>> >>> [...] >>> >>> Getting Loaded... >>> Reading file topol.tpr, VERSION 4.0.4 (single precision) >>> Loaded with Money >>> >>> Steepest Descents: >>> Tolerance (Fmax) = 1.0e+01 >>> Number of steps = 1 >>> Step= 1, Dmax= 1.0e-02 nm, Epot= 1.23314e+20 Fmax= 2.04950e+19, atom= >>> 11163 >>> Step= 2, Dmax= 1.2e-02 nm, Epot= 5.22616e+17 Fmax= 2.22256e+20, atom= >>> 10863 >>> Step= 3, Dmax= 1.4e-02 nm, Epot= 1.46382e+17 Fmax= 7.52962e+17, atom= >>> 10593 >>> Step= 4, Dmax= 1.7e-02 nm, Epot= 1.21703e+17 Fmax= 3.72098e+16, atom= >>> 10331 >>> Step= 5, Dmax= 2.1e-02 nm, Epot= 2.22862e+16 Fmax= 4.87326e+18, atom= >>> 10857 >>> Step= 6, Dmax= 2.5e-02 nm, Epot= 1.09032e+16 Fmax= 4.39937e+15, atom= >>> 15106 >>> Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81517e+15 Fmax= 6.07049e+14, atom= >>> 15230 >>> Step= 8, Dmax= 3.6e-02 nm, Epot= 2.84750e+14 Fmax= 9.82848e+14, atom= >>> 14675 >>> Step= 9, Dmax= 4.3e-02 nm, Epot= 2.33131e+14 Fmax= 2.39469e+13, atom= >>> 11419 >>> Step= 10, Dmax= 5.2e-02 nm, Epot= 7.23189e+12 Fmax= 2.72305e+14, atom= >>> 14565 >>> Step= 11, Dmax= 6.2e-02 nm, Epot= 3.19510e+12 Fmax= 4.82192e+12, atom= >>> 10638 >>> Step= 13, Dmax= 3.7e-02 nm, Epot= 1.82616e+12 Fmax= 1.11184e+13, atom= >>> 11929 >>> [... etc.] >>> <<< >>> >>> This is a minimization using the steepest descent algorithm. What am I >>> doing wrong here? >>> >>> Thank you in advance for your kind help! >>> >> >> If you use default names (i.e., topol.tpr for output), you can easily confuse >> yourself and wind up running the w
RE: [gmx-users] Problem with grompp?
Hi Justin, Thanks for your answer. I am afraid, however, that the problem is then somewhat different. Using grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 should have created a new topol.tpr, should it not? It did so in previous times at least. If someone knows where I am going wrong, please let me know. Kind regards, Bram -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: woensdag 15 april 2009 18:12 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Problem with grompp? Hoof, B. van wrote: > Hi everyone, > > Since I am a new user of Gromacs, this problem is probably rather trivial, > but I hope one of you would like to help me nonetheless. I have created a > starting structure in a not very optimal situation, which I have then > minimized. To continue, I would like to equilibrate the system further using > leap-frog MD. To do so, I have used grompp in the following way: > grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 > > This creates the following mdout.mdp: see attachment > > Now as far as I can see, using the command `mdrun -v -c md_run.gro' should > result in performing a 1,000,000 iteration md simulation of this system. > However, when I issue that command, instead what I get is this: > :-) G R O M A C S (-: > > Good ROcking Metal Altar for Chronical Sinners > > :-) VERSION 4.0.4 (-: > > > [...] > > :-) mdrun (-: > > Option Filename Type Description > > [...] > > Getting Loaded... > Reading file topol.tpr, VERSION 4.0.4 (single precision) > Loaded with Money > > Steepest Descents: >Tolerance (Fmax) = 1.0e+01 >Number of steps=1 > Step=1, Dmax= 1.0e-02 nm, Epot= 1.23314e+20 Fmax= 2.04950e+19, atom= > 11163 > Step=2, Dmax= 1.2e-02 nm, Epot= 5.22616e+17 Fmax= 2.22256e+20, atom= > 10863 > Step=3, Dmax= 1.4e-02 nm, Epot= 1.46382e+17 Fmax= 7.52962e+17, atom= > 10593 > Step=4, Dmax= 1.7e-02 nm, Epot= 1.21703e+17 Fmax= 3.72098e+16, atom= > 10331 > Step=5, Dmax= 2.1e-02 nm, Epot= 2.22862e+16 Fmax= 4.87326e+18, atom= > 10857 > Step=6, Dmax= 2.5e-02 nm, Epot= 1.09032e+16 Fmax= 4.39937e+15, atom= > 15106 > Step=7, Dmax= 3.0e-02 nm, Epot= 1.81517e+15 Fmax= 6.07049e+14, atom= > 15230 > Step=8, Dmax= 3.6e-02 nm, Epot= 2.84750e+14 Fmax= 9.82848e+14, atom= > 14675 > Step=9, Dmax= 4.3e-02 nm, Epot= 2.33131e+14 Fmax= 2.39469e+13, atom= > 11419 > Step= 10, Dmax= 5.2e-02 nm, Epot= 7.23189e+12 Fmax= 2.72305e+14, atom= > 14565 > Step= 11, Dmax= 6.2e-02 nm, Epot= 3.19510e+12 Fmax= 4.82192e+12, atom= > 10638 > Step= 13, Dmax= 3.7e-02 nm, Epot= 1.82616e+12 Fmax= 1.11184e+13, atom= > 11929 > [... etc.] > <<< > > This is a minimization using the steepest descent algorithm. What am I doing > wrong here? > > Thank you in advance for your kind help! > If you use default names (i.e., topol.tpr for output), you can easily confuse yourself and wind up running the wrong input file. The mdout.mdp file you posted should correspond to MD; most likely you've just re-run the same .tpr file that you used for minimization. -Justin > Greetings, > Bram van Hoof > > > > > > > > > ___ > 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 Graduate Research Assistant 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-u
RE: [gmx-users] Problem with grompp?
Yes, indeed. The file topol.tpr was not re-created when I used grompp. In fact, an error was thrown by grompp stating file input/output error: minimized.gro I am embarrased to say that I had used the command > grompp -f martini_md1.mdp -c minimized.gro -p martini.top -o membr.tpr > -maxwarn 10 instead of > grompp -f martini_md1.mdp -c minimised.gro -p martini.top -o membr.tpr > -maxwarn 10 Unfortunately, because mdout.mdp was created correctly, I hadn't noticed this error. Thank you everyone for your help! Bram van Hoof -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar Sent: donderdag 16 april 2009 12:11 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Problem with grompp? Hi Bram, Check the creation times for topol.tpr and minimized.gro. First test the assumption that the former was created later than the latter. If it's not, then check the grompp output for errors. Maybe pasting it here can help. Cheers, Tsjerk On Thu, Apr 16, 2009 at 10:57 AM, Hoof, B. van wrote: > Hi Justin, > > Thanks for your answer. I am afraid, however, that the problem is then > somewhat different. Using > grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 > should have created a new topol.tpr, should it not? It did so in previous > times at least. > > If someone knows where I am going wrong, please let me know. > > Kind regards, > Bram > > > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On > Behalf Of Justin A. Lemkul > Sent: woensdag 15 april 2009 18:12 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Problem with grompp? > > > > Hoof, B. van wrote: >> Hi everyone, >> >> Since I am a new user of Gromacs, this problem is probably rather trivial, >> but I hope one of you would like to help me nonetheless. I have created a >> starting structure in a not very optimal situation, which I have then >> minimized. To continue, I would like to equilibrate the system further using >> leap-frog MD. To do so, I have used grompp in the following way: >> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10 >> >> This creates the following mdout.mdp: see attachment >> >> Now as far as I can see, using the command `mdrun -v -c md_run.gro' should >> result in performing a 1,000,000 iteration md simulation of this system. >> However, when I issue that command, instead what I get is this: >> :-) G R O M A C S (-: >> >> Good ROcking Metal Altar for Chronical Sinners >> >> :-) VERSION 4.0.4 (-: >> >> >> [...] >> >> :-) mdrun (-: >> >> Option Filename Type Description >> >> [...] >> >> Getting Loaded... >> Reading file topol.tpr, VERSION 4.0.4 (single precision) >> Loaded with Money >> >> Steepest Descents: >> Tolerance (Fmax) = 1.0e+01 >> Number of steps = 1 >> Step= 1, Dmax= 1.0e-02 nm, Epot= 1.23314e+20 Fmax= 2.04950e+19, atom= >> 11163 >> Step= 2, Dmax= 1.2e-02 nm, Epot= 5.22616e+17 Fmax= 2.22256e+20, atom= >> 10863 >> Step= 3, Dmax= 1.4e-02 nm, Epot= 1.46382e+17 Fmax= 7.52962e+17, atom= >> 10593 >> Step= 4, Dmax= 1.7e-02 nm, Epot= 1.21703e+17 Fmax= 3.72098e+16, atom= >> 10331 >> Step= 5, Dmax= 2.1e-02 nm, Epot= 2.22862e+16 Fmax= 4.87326e+18, atom= >> 10857 >> Step= 6, Dmax= 2.5e-02 nm, Epot= 1.09032e+16 Fmax= 4.39937e+15, atom= >> 15106 >> Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81517e+15 Fmax= 6.07049e+14, atom= >> 15230 >> Step= 8, Dmax= 3.6e-02 nm, Epot= 2.84750e+14 Fmax= 9.82848e+14, atom= >> 14675 >> Step= 9, Dmax= 4.3e-02 nm, Epot= 2.33131e+14 Fmax= 2.39469e+13, atom= >> 11419 >> Step= 10, Dmax= 5.2e-02 nm, Epot= 7.23189e+12 Fmax= 2.72305e+14, atom= >> 14565 >> Step= 11, Dmax= 6.2e-02 nm, Epot= 3.19510e+12 Fmax= 4.82192e+12, atom= >> 10638 >> Step= 13, Dmax= 3.7e-02 nm, Epot= 1.82616e+12 Fmax= 1.11184e+13, atom= >> 11929 >> [... etc.] >> <<< >> >> This is a minimization using the steepest descent algorithm. What am I doing >> wrong here? >> >> Thank you in advance for your kind help! >> > > If you use default names (i.e., topol.tpr for output), you can easily confuse > yourself and wind up running the wrong input file. The mdout.mdp file you > posted should correspond to MD; most likely you've just re-run the same .tpr > file that you used for minimization. > > -Justin > >> Greetings, >> Bram van Hoof >> >> >> >> >> >> >> >> >> ___ >> 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 po
[gmx-users] the vdw and electrostatic energy
Dear all, When we do a MD simulation, we always set a cutoff of non-bonded interactions, e.g. r=1.2 nm. When the simulation finished, we can use the command g_energy -f ener.edr -s ... to abtain the non-boned energy of the system. My question is whether the non-bonded energy values dependent on the non-bonded cutoff? If YES, there may be no problem of the vdw interaction (LJ-SR), because the vdw interaction vanish in a short distance. But how about the electrostatic term with the distance dependence of 1/r^2 ? Best regards, = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lidc02 at mails.tsinghua.edu.cn = ___ 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] the vdw and electrostatic energy
Hi, This problem has been discussed for decades in the literature. There are approaches such as PME and reaction field to deal with the long-range electrostatics. Ran. Dechang Li wrote: > Dear all, > > When we do a MD simulation, we always set a cutoff > of non-bonded interactions, e.g. r=1.2 nm. When the > simulation finished, we can use the command > g_energy -f ener.edr -s ... to abtain the non-boned > energy of the system. My question is whether the non-bonded > energy values dependent on the non-bonded cutoff? If YES, > there may be no problem of the vdw interaction (LJ-SR), > because the vdw interaction vanish in a short distance. But > how about the electrostatic term with the distance dependence > of 1/r^2 ? > > > > Best regards, > > > > = > Dechang Li, Ph.D Candidate > Department of Engineering Mechanics > Tsinghua University > Beijing 100084 > P.R. China > > Tel: +86-10-62773574(O) > Email: lidc02 at mails.tsinghua.edu.cn > = > > > > ___ > 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 > > -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ 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] pull code absolute reference artifacts
Hello, I have a question about the following grompp 4.0.4 warning: "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts." While I do realize that this is an excellent error message containing lots of information, I am still unclear about how to proceed. Why does my system not have an absolute reference? Is it because I have pbc and center of mass motion removal? Exactly what types of artifacts are expected? Is there a simple solution? I am trying to hold my peptide in the center of a water box. I realize that there is no "center" and everything in pbc, but I need to do it nevertheless. Here are my .mdp options: pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_ngroups= 1 ;pull_group0 = pull_group1 = peptide_A pull_k1 = 500 pull_init1 = 0.00 nsteps = 25 ; REMOVE_FOR_EM tinit = 49000 ; REMOVE_FOR_EM dt = 0.004 ; REMOVE_FOR_EM nstxout = 25 ; REMOVE_FOR_EM nstvout = 25 ; REMOVE_FOR_EM nstfout = 25 ; REMOVE_FOR_EM nstenergy = 25000 ; REMOVE_FOR_EM nstxtcout = 25000 ; REMOVE_FOR_EM nstlog = 25; REMOVE_FOR_EM gen_vel = no unconstrained-start = yes integrator = sd gen_seed= -1 comm_mode = linear nstcomm = 1 comm_grps = System nstlist = 5 ns_type = grid pbc = xyz coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 DispCorr= EnerPres Pcoupl = Berendsen ; REMOVE_FOR_EM pcoupltype = isotropic ; REMOVE_FOR_EM compressibility = 4.5e-5 ; REMOVE_FOR_EM ref_p = 1. ; REMOVE_FOR_EM tau_p = 4.0; REMOVE_FOR_EM tc_grps = System ; REMOVE_FOR_EM tau_t = 1.0; REMOVE_FOR_EM ld_seed = -1 ; REMOVE_FOR_EM ref_t = 300. ; REMOVE_FOR_EM gen_temp= 300. ; REMOVE_FOR_EM constraints = all-bonds ; REMOVE_FOR_EM constraint_algorithm= lincs ; REMOVE_FOR_EM lincs-iter = 1 ; REMOVE_FOR_EM lincs-order = 6 ; REMOVE_FOR_EM ___ 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] Temperature in Brownian Dynamics simulation
Hi, it was pointed out before that for Brownian Dynamics simulation, the temperature calculated by g_energy does not match with the ref_t in parameter file and it is almost double: http://www.gromacs.org/pipermail/gmx-users/2007-June/028321.html ... but unfortunately I find no follow-up to that post. So I want to ask the question again here. I am doing Brownian Dynamics simulation of a single polymer chain consisting of 100 atoms. While I have set 300K as my simulation temperature, when I try to use g_energy to check the temperature it reports the following: Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 624.18844.086244.0862 -1.52693e-06 -0.152693 T-Protein 624.18844.086244.0862 -1.52693e-06 -0.152693 Here is the content of my mdp file: = integrator = bd dt = 0.002; ps ! nsteps = 5000 ; total 100 ns. nstxout = 1000 nstvout = 0 nstfout = 0 nstlist = 10 nstlog = 100 rlist = 1.0 rvdw= 1.0 bd_fric = 0 ld_seed = -1 constraints = all-bonds lincs_order = 8 lincs_iter = 8 Tcoupl = no tau_t = 0.01 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 = Please help me troubleshoot this problem. Thanks. Best regards, Suman Chakrabarty. ___ 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] Re:Re: the vdw and electrostatic energy (Ran Friedman)
>-- > >Message: 3 >Date: Thu, 16 Apr 2009 14:11:51 +0200 >From: Ran Friedman >Subject: Re: [gmx-users] the vdw and electrostatic energy >To: Discussion list for GROMACS users >Message-ID: <49e72087.8020...@bioc.uzh.ch> >Content-Type: text/plain; charset=GB2312 > >Hi, > >This problem has been discussed for decades in the literature. There are >approaches such as PME and reaction field to deal with the long-range >electrostatics. I did not mean that. I want to know that when we use g_energy in Gromacs to read the energy from the file ener.edr, does the cutoff affect the values of the energy? For example, when the cutoff is set to 1.2 nm and the PME method is used, does the energy term "Coul-SR" read by g_energy contain the long range part ? > >Ran. > >Dechang Li wrote: >> Dear all, >> >> When we do a MD simulation, we always set a cutoff >> of non-bonded interactions, e.g. r=1.2 nm. When the >> simulation finished, we can use the command >> g_energy -f ener.edr -s ... to abtain the non-boned >> energy of the system. My question is whether the non-bonded >> energy values dependent on the non-bonded cutoff? If YES, >> there may be no problem of the vdw interaction (LJ-SR), >> because the vdw interaction vanish in a short distance. But >> how about the electrostatic term with the distance dependence >> of 1/r^2 ? >> >> >> >> Best regards, >> >> >> >> = >> Dechang Li, Ph.D Candidate >> Department of Engineering Mechanics >> Tsinghua University >> Beijing 100084 >> P.R. China >> >> Tel: +86-10-62773574(O) >> Email: lidc02 at mails.tsinghua.edu.cn >> > > ___ 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] Re:Re: the vdw and electrostatic energy (Ran Friedman)
No. SR stands for short-range. Ran. > > I did not mean that. I want to know that when we use g_energy in > Gromacs to > read the energy from the file ener.edr, does the cutoff affect the values > of the energy? For example, when the cutoff is set to 1.2 nm and the PME > method > is used, does the energy term "Coul-SR" read by g_energy contain the long > range > part ? > ___ 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] Installing topolbuild
Apparently some versions of make do not handle my make files the same way that the version of make I use does. The attached Makefile might help in such cases. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 Makefile Description: Binary data ___ 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] pull code absolute reference artifacts
Hi Justin: 1) EXTREMELY IMPORTANT: I already know of 1 person, but is anyone alergic to either Iodine or Chlorine? No, I am not alergic to those compounds. The only thing that I am alergic is Penicillin and Ampicilin. 2) Any other medical problems? No 3) An Emergency contact person. Fernando Babilonia. Telf: 646 752 6557 4) What food are you planning on bringing? If anyone is planning on bringing food that needs to be heated, cooked, or boiled i need to re-calculate how much fuel we need for the stove incase the rain prevents us from lighting a fire. I am planning to take fast easy food like tuna or sandwiches. The only thing that i am planning to use heat is to boil water for instant tea and also I planning to have some hotdogs at dinner. -Rodney ___ 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] strange behavior upon compiling 4.0.4
Hello all, I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro running 10.5. The program configures with out a hitch, but compiling with the make command ends in a recursive error. It seems that it's not finding something that it should have installed itself, but I wouldn't be surprised if I was wrong. Any ideas? Thanks, Ken mkdir .libs rm -fr .libs/libnonbonded.lax mkdir .libs/libnonbonded.lax rm -fr .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a mkdir .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a Extracting /Users/jkoelmel/Desktop/college and IB/college/current classes/BioChem/GROMACS/gromacs-4.0.4/src/gmxlib/nonbonded/ nb_kernel_ia32_sse/.libs/libnb_kernel_ia32_sse.a (cd .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a && ar x /Users/jkoelmel/Desktop/college and IB/college/current classes/BioChem/GROMACS/gromacs-4.0.4/src/gmxlib/nonbonded/ nb_kernel_ia32_sse/.libs/libnb_kernel_ia32_sse.a) ar: /Users/jkoelmel/Desktop/college: No such file or directory make[5]: *** [libnonbonded.la] Error 1 make[4]: *** [all-recursive] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 Dr. KS Rotondi The Departments of Chemistry & Biochemistry and Molecular Biology The University of Massachusetts - Amherst 815B LGRT Amherst, MA 01075 k...@chemistry.umass.edu Phone: 413-545-1591 Fax:413-545-4490 "If there's a solution, why worry? If there's no solution, why worry?" The Dali Lama ___ 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] strange behavior upon compiling 4.0.4
Ken Rotondi wrote: Hello all, I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro running 10.5. The program configures with out a hitch, but compiling with the make command ends in a recursive error. It seems that it's not finding something that it should have installed itself, but I wouldn't be surprised if I was wrong. Any ideas? Could be because there is a space in a directory name. Thanks, Ken mkdir .libs rm -fr .libs/libnonbonded.lax mkdir .libs/libnonbonded.lax rm -fr .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a mkdir .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a Extracting /Users/jkoelmel/Desktop/college and IB/college/current classes/BioChem/GROMACS/gromacs-4.0.4/src/gmxlib/nonbonded/nb_kernel_ia32_sse/.libs/libnb_kernel_ia32_sse.a (cd .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a && ar x /Users/jkoelmel/Desktop/college and IB/college/current classes/BioChem/GROMACS/gromacs-4.0.4/src/gmxlib/nonbonded/nb_kernel_ia32_sse/.libs/libnb_kernel_ia32_sse.a) ar: /Users/jkoelmel/Desktop/college: No such file or directory make[5]: *** [libnonbonded.la] Error 1 make[4]: *** [all-recursive] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 Dr. KS Rotondi The Departments of Chemistry & Biochemistry and Molecular Biology The University of Massachusetts - Amherst 815B LGRT Amherst, MA 01075 k...@chemistry.umass.edu Phone:413-545-1591 Fax:413-545-4490 "If there's a solution, why worry? If there's no solution, why worry?" The Dali Lama ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ 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] strange behavior upon compiling 4.0.4
Ken Rotondi wrote: Hello all, I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro running 10.5. The program configures with out a hitch, but compiling with the make command ends in a recursive error. It seems that it's not finding something that it should have installed itself, but I wouldn't be surprised if I was wrong. Any ideas? Thanks, Ken mkdir .libs rm -fr .libs/libnonbonded.lax mkdir .libs/libnonbonded.lax rm -fr .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a mkdir .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a Extracting /Users/jkoelmel/Desktop/college and IB/college/current classes/BioChem/GROMACS/gromacs-4.0.4/src/gmxlib/nonbonded/nb_kernel_ia32_sse/.libs/libnb_kernel_ia32_sse.a (cd .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a && ar x /Users/jkoelmel/Desktop/college and IB/college/current classes/BioChem/GROMACS/gromacs-4.0.4/src/gmxlib/nonbonded/nb_kernel_ia32_sse/.libs/libnb_kernel_ia32_sse.a) ar: /Users/jkoelmel/Desktop/college: No such file or directory I'll lead off with the obvious dumb question - does this particular directory exist on the student's machine? -Justin make[5]: *** [libnonbonded.la] Error 1 make[4]: *** [all-recursive] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 Dr. KS Rotondi The Departments of Chemistry & Biochemistry and Molecular Biology The University of Massachusetts - Amherst 815B LGRT Amherst, MA 01075 k...@chemistry.umass.edu Phone:413-545-1591 Fax:413-545-4490 "If there's a solution, why worry? If there's no solution, why worry?" The Dali Lama ___ 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 thewww 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
Re: [gmx-users] strange behavior upon compiling 4.0.4
Yes sir, that was the problem Many thanks, Ken On Apr 16, 2009, at 3:33 PM, David van der Spoel wrote: Ken Rotondi wrote: Hello all, I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro running 10.5. The program configures with out a hitch, but compiling with the make command ends in a recursive error. It seems that it's not finding something that it should have installed itself, but I wouldn't be surprised if I was wrong. Any ideas? Could be because there is a space in a directory name. Thanks, Ken mkdir .libs rm -fr .libs/libnonbonded.lax mkdir .libs/libnonbonded.lax rm -fr .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a mkdir .libs/libnonbonded.lax/libnb_kernel_ia32_sse.a Extracting /Users/jkoelmel/Desktop/college and IB/college/current classes/BioChem/GROMACS/gromacs-4.0.4/src/gmxlib/nonbonded/ nb_kernel_ia32_sse/.libs/libnb_kernel_ia32_sse.a (cd .libs/ libnonbonded.lax/libnb_kernel_ia32_sse.a && ar x /Users/jkoelmel/Desktop/college and IB/college/current classes/BioChem/GROMACS/gromacs-4.0.4/src/gmxlib/nonbonded/ nb_kernel_ia32_sse/.libs/libnb_kernel_ia32_sse.a) ar: /Users/ jkoelmel/Desktop/college: No such file or directory make[5]: *** [libnonbonded.la] Error 1 make[4]: *** [all-recursive] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 Dr. KS Rotondi The Departments of Chemistry & Biochemistry and Molecular Biology The University of Massachusetts - Amherst 815B LGRT Amherst, MA 01075 k...@chemistry.umass.edu Phone:413-545-1591 Fax:413-545-4490 "If there's a solution, why worry? If there's no solution, why worry?" The Dali Lama ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ 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] Non-equilibrium Viscosity Calculation
Dear All: I wanted to get the viscosity of my simulated polymer system. From the manual it said that : GROMACS also has a non-equilibrium method for determining the viscosity" (page 123) Does this mean I just need to do a separate non-equilibrium MD run? In terms of mdp file, I just need to add the following options, right? acc_grps: accelerate: cos_acceleration: My question is: first, how to set the value of cos_acceleration: ? Second, after I finish the run, how can I get the viscosity from the simulation result? Anyone has done this yet? Thank you so much for your answer 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] The way how to restrict atoms in gromacs
Hi all users, I have used the position_restraints to restrict some atoms' activity but always it shows that Segmentation fault (core dumped). I can not fix this problem after trying many methods and hence, I just wonder whether there are some other ways to restrict the atoms' movement in the gromacs. Any suggestions will be highly appreciated . Yang ___ 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] The way how to restrict atoms in gromacs
He, Yang wrote: Hi all users, I have used the position_restraints to restrict some atoms' activity but always it shows that Segmentation fault (core dumped). It's 99% likely that this is not all that is going on - you have to read the end of the .log file and the standard output/error to diagnose what is going wrong. A segmentation fault is just a general expression that the software encountered an invalid memory reference - it can't help someone diagnose the cause. GROMACS almost always gives a real diagnostic message before doing so. I can not fix this problem after trying many methods and hence, I just wonder whether there are some other ways to restrict the atoms' movement in the gromacs. There many sorts of restraints, there are freeze groups and there are constraints. Have a look in the manual. Mark ___ 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] Temperature in Brownian Dynamics simulation
Suman Chakrabarty wrote: Hi, it was pointed out before that for Brownian Dynamics simulation, the temperature calculated by g_energy does not match with the ref_t in parameter file and it is almost double: http://www.gromacs.org/pipermail/gmx-users/2007-June/028321.html ... but unfortunately I find no follow-up to that post. So I want to ask the question again here. I am doing Brownian Dynamics simulation of a single polymer chain consisting of 100 atoms. While I have set 300K as my simulation temperature, I don't think you have. You've generated velocities at that temperature, but you're not thermostatting to that temperature, since you have "Tcoupl = no" Mark when I try to use g_energy to check the temperature it reports the following: Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 624.18844.086244.0862 -1.52693e-06 -0.152693 T-Protein 624.18844.086244.0862 -1.52693e-06 -0.152693 Here is the content of my mdp file: = integrator = bd dt = 0.002; ps ! nsteps = 5000 ; total 100 ns. nstxout = 1000 nstvout = 0 nstfout = 0 nstlist = 10 nstlog = 100 rlist = 1.0 rvdw= 1.0 bd_fric = 0 ld_seed = -1 constraints = all-bonds lincs_order = 8 lincs_iter = 8 Tcoupl = no tau_t = 0.01 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 = Please help me troubleshoot this problem. Thanks. Best regards, Suman Chakrabarty. ___ 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] calculating com-com distances.
Tsjerk, your good reference helped me to understand the set_pbc and pbc_dx functions from g_dist... I changed few lines of it and my problem was solved. Thank you. Cheers. Fernando. 2009/4/14 Tsjerk Wassenaar > Hi Fernando, > > Just bear in mind that these lattice vectors are just translation > vectors. You can add them to or subtract them from the positional > vectors of the com. That way you'll get a number of points which you > can use to calculate the distances the regular way. To see where you > went wrong, consider that a vector of the triclinic unit cell may have > more than one non-zero component. You considered only one non-zero > component, based upon the rectangular brick representation. But from > Pythagoras theorem it follows that doing so will make you miss part of > the true distance and come to an underestimate of it. > There is a niftier solution to the smallest distance, which will work > regardless of the separation between particles/coms in the infinite > system. It's in my thesis (Chapter 3, Appendix C, page 68): > > http://dissertations.ub.rug.nl/faculties/science/2006/t.a.wassenaar/?FullItemRecord=ON > > Hope it helps, > > Tsjerk > > On 4/14/09, Fernando C wrote: > > Hi Tsjerk and all list! > > > > > You have to use the three vectors from the tricilinic representation > > > to obtain the correct distance in the periodic system. Check PBC in > > > Chapter 3 of the manual. > > > > > > I used the length values from rectangular box because I'd want believe > that > > my problem would be solved easily; I wouldn't want to fall in question of > > calculate positions and distances in triclinic cells. But here I am: > could > > anybody explain to me the algorithm of how such things are calculated? > > > > Thanks again! > > > > Fernando. > > > > > > > > > > > > -- > > And Noel Gallagher said: Gromacs is gonna live forever! > > > > 2009/4/13 Tsjerk Wassenaar > > > > > > Hi Fernando, > > > > > > > > > > I've obtained the vectors for the rectangular box in g_energy, > > > > using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of > the > > > > skewed box.) > > > > > > You have to use the three vectors from the tricilinic representation > > > to obtain the correct distance in the periodic system. Check PBC in > > > Chapter 3 of the manual. > > > > > > Cheers, > > > > > > Tsjerk > > > > > > -- > > > 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 > > > > > -- > 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
[gmx-users] query
Dear gmx users,
While running final md run some unexpected message is coming which i am not
able to understand..
Pls help.
I am attaching md.log file with this mail.
--
Sheetal Arora
M.Tech(Biotechnology & Medical Engg)
NIT Rourkela
Log file opened on Fri Apr 17 09:37:41 2009
Host: localhost1.localdomain pid: 3293 nodeid: 0 nnodes: 1
The Gromacs distribution was built Fri Mar 20 17:46:50 IST 2009 by
r...@localhost.localdomain (Linux 2.6.18-53.el5PAE i686)
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Input Parameters:
integrator = md
nsteps = 50
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 5000
nstxout = 2500
nstvout = 5000
nstfout = 0
nstenergy= 500
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 88
nky = 88
nkz = 88
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart= FALSE
bShakeSOR= FALSE
etc = Berendsen
epc = No
epctype = Isotropic
tau_p= 0.5
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
andersen_seed= 815131
rlist= 1.4
coulombtype = PME
rcoulomb_switch = 0.8
rcoulomb = 1.4
vdwtype = Cut-off
rvdw_switch = 0.8
rvdw = 1.4
epsilon_r= 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 1
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau= 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Shake
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 =
Re: [gmx-users] query
Sheetal Arora wrote: Dear gmx users, While running final md run some unexpected message is coming which i am not able to understand.. Pls help. I am attaching md.log file with this mail. That's just normal output with no diagnostic message about the reason for incomplete termination - if indeed that is happening. Without a more full description of what you're trying to achieve and the contents of standard error/output we won't be able to help you further. Mark ___ 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] Non-equilibrium Viscosity Calculation
Yanmei Song wrote: Dear All: I wanted to get the viscosity of my simulated polymer system. From the manual it said that : GROMACS also has a non-equilibrium method for determining the viscosity" (page 123) Does this mean I just need to do a separate non-equilibrium MD run? In terms of mdp file, I just need to add the following options, right? acc_grps: accelerate: cos_acceleration: Just the last one. My question is: first, how to set the value of cos_acceleration: ? You need to do a few values such that you can extrapolate to zero acceleration. Second, after I finish the run, how can I get the viscosity from the simulation result? Anyone has done this yet? Thank you so much for your answer in advance. g_energy. J Chem Phys 116 (2002) 209-217 J Chem Phys 119 (2003) 7308-7317 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ 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
