RE: [gmx-users] g_polystat
> Date: Sat, 4 Sep 2010 17:50:46 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] g_polystat > > > > Moeed wrote: > > Hello Justin, > > > > I have read help of the command I am using several times. My > > understanding is that g_polystat calculates Rg of 8 chains and takes the > > average if no specific index groups are selected. Below are the groups I > > have created for 8 chains. > > g_polystat -f *.trr -s *.tpr -o polystat-mw-xvgr-8group -n *.ndx -mw > > -xvgr -w -p persist.xvg > > then chose 0 1 2 3 4 5 6 7 as se;ected groups. The point is Rg for this > > 8 molecules is similar to that When I select group 0 only. If Rg is the > > average of all chians over time why is it giving Rg of first chain? > > > > g_polystat does not accept multiple input groups, so if you're entering "0 1 > 2 > 3..." at the index prompt, then only group 0 is selected. The tool will > print > which group it is analyzing. I think this is generally true for all Gromacs > tools. Try analyzing a group that contains all your polymers. > > > Also as for persistence lenght -h option says: > > The chosen index group > > should consist of atoms that are consecutively bonded in the polymer > > mainchains. My groups start from atom 1 to 8*362 consecutively... Do you > > any clue why I am mot getting output file? > > > > Not really. But if you're including all atoms in the analysis, then you're > not > analyzing main chain atoms, as the tool expects. Try creating an index group > of > only one molecule, and only its main chain (presumably non-H) atoms. From > the > description, it also sounds like the group selected should contain "atoms > that > are consecutively bonded." Whether or not that excludes the possibility of > analyzing multiple molecules at once, I don't know, but atoms that are not > consecutively bonded should not be included in the analysis. For the radius of gyration you can choose any group you like. For the persistence length the programs compares directions of vectors between consecutive atoms in the index group, so you usually want only atoms in the main chain for that (no hydrogens etc). As the manual says, the selected group is split into molecules, it will always analyze every molecule separately and average the results. Berk > > -Justin > > > > > Group 0 ( PE60-1) has 362 elements > > Group 1 ( PE60-2) has 362 elements > > Group 2 ( PE60-3) has 362 elements > > Group 3 ( PE60-4) has 362 elements > > Group 4 ( PE60-5) has 362 elements > > Group 5 ( PE60-6) has 362 elements > > Group 6 ( PE60-7) has 362 elements > > Group 7 ( PE60-8) has 362 elements > > > > Thank you > > > > -- > > > 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/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] Protein stability using MARTINI
- Original Message - From: Itamar Kass Date: Monday, September 6, 2010 14:06 Subject: [gmx-users] Protein stability using MARTINI To: Discussion list for GROMACS users > HI all, > > I am simulating a protein in water using the MARTINI (CG) force > field. My protein composed of few alpha-helices and a big tail > (~50AA) which is random coiled. I have built the simulation > system according to the procedure at > http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in- > water . > > After a 10ns simulation, I have visualised the system using VMD. > It seems like the protein had dismantled to amino acids. I see > groups of bids moving freely in the system. I'm not sure what you mean here, but it seems likely that VMD's heuristics for guessing where bonds between atoms might exist aren't going to work well for a coarse-grained protein. There's probably a standard solution, for which you should Google :-) Mark > > Any idea of the problem? Any idea how to fix it? > > PS I don't want to use elastic network for the random coil tail, > as I wish to capture as much conformation as possible. > > Thanks in advance, > Itamar. > > -- > > > "In theory, there is no difference between theory and practice. > But, in practice, there is." - Jan L.A. van de Snepscheut > > === > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu > > > -- > 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] the broken of the molecules
Hello, I do the energy minimization of the butylene box , but some butylene molecules are broken after that. The butylene itp file is produced by PRODRG, as follows: [ moleculetype ] ; Name nrexcl BUT 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 BUT C9 1 0.0049 15.0350 2 CH2 1 BUT C6 1 -0.02442 14.0270 3 C 1 BUT C3 1 0.07957 13.0190 4 C 1 BUT C2 1 -0.06005 14.0270 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.155 715.0 0.155 715.0 ; C6 C9 2 3 2 0.153 715.0 0.153 715.0 ; C6 C3 3 4 2 0.135 715.0 0.135 715.0 ; C3 C2 [ pairs ] ; ai aj fu c0, c1, ... 1 4 1 ; C9 C2 [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 112.5 520.0 112.5 520.0 ; C9 C6 C3 2 3 4 2 125.0 610.0 125.0 610.0 ; C6 C3 C2 [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 1 2 3 4 1 0.0 1.0 6 0.0 1.0 6 ; dih C9 C6 C3 C2 Can you show me why the butylene molecules would be broken? Thank you very much ! -- 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] the broken of the molecules
Hi, If I guess you correctly, you probably mean that when you look on your results (using VMD) it seems like it broken. If this is the case, you are OK, it might seems so but it is not, if you indeed used PBC. Best, Itamar On 6/09/2010 6:25 PM, kecy...@sina.com wrote: Hello, I do the energy minimization of the butylene box , but some butylene molecules are broken after that. The butylene itp file is produced by PRODRG, as follows: /[ moleculetype ] ; Name nrexcl BUT 3/ /[ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 BUT C9 1 0.0049 15.0350 2 CH2 1 BUT C6 1 -0.02442 14.0270 3 C 1 BUT C3 1 0.07957 13.0190 4 C 1 BUT C2 1 -0.06005 14.0270 / /[ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.155 715.0 0.155 715.0 ; C6 C9 2 3 2 0.153 715.0 0.153 715.0 ; C6 C3 3 4 2 0.135 715.0 0.135 715.0 ; C3 C2 / /[ pairs ] ; ai aj fu c0, c1, ... 1 4 1 ; C9 C2 / /[ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 112.5 520.0 112.5 520.0 ; C9 C6 C3 2 3 4 2 125.0 610.0 125.0 610.0 ; C6 C3 C2 / /[ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 1 2 3 4 1 0.0 1.0 6 0.0 1.0 6 ; dih C9 C6 C3 C2 / // Can you show me why the butylene molecules would be broken? Thank you very much ! // -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] grompp_d and mdrun_d issues with GBSA and normal mode analysis
Dear GROMACS users, I am encountering a couple of issues when trying to perform normal mode analysis in an implicit solvent (GBSA) setting. I am using version 4.5.1 with double precision; unfortunately I do not have the single precision version installed for comparison. The starting point is a small protein which was energy minimized in two stages, also in double precision and with GBSA, producing "em2" files. The mdp file used for the normal mode analysis is the following: - nm.mdp - integrator = nm nsteps = 1 implicit_solvent = GBSA gb_algorithm = Still ; the default rgbradii = 1.0 ; must be equal to rlist rlist= 1.0 coulombtype = cut-off rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 --- The command used is grompp_d -f nm.mdp -p topol.top -c em2.gro -t em2.trr -o nm.tpr which ran fine except for the following note: NOTE 1 [file nm.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Then, I tried to run mdrun_d -v -nice 0 -deffnm nm However, the command seems to be stuck, and the following serious warning is produced: Warning: 1-4 interaction between 64 and 71 at distance 3.114 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Maximum force: 3.48709e+06 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. The em2.gro is definitely not having such a large distance between atoms 64 and 71: 6GLN CB 64 1.879 1.895 2.423 . . 6GLNOE1 71 2.047 1.715 2.642 which are only about 0.346 nm apart. Also, the energy minimization, which used the same options, mutatis mutandis, -- em2.mdp -- integrator = cg nsteps = 1000 nstcgsteep = 40 implicit_solvent = GBSA gb_algorithm = Still ; the default rgbradii = 1.0 ; must be equal to rlist nstlist = 10 rlist= 1.0 coulombtype = cut-off rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 nstenergy= 10 - converged to machine precision having a much smaller maximum force: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Polak-Ribiere Conjugate Gradients converged to machine precision in 0 steps, but did not reach the requested Fmax < 10. Potential Energy = -2.71868395521758e+04 Maximum force = 4.63436548427712e+02 on atom 584 Norm of force = 1.25296847735530e+02 The other problem arises when I try to follow the grompp_d note above and change in nm.mdp to coulombtype = pme I then have a fatal error: ERROR 1 [file nm.mdp]: With GBSA, coulombtype must be equal to Cut-off Am I doing something wrong or are there still some problems in the new GBSA option of version 4.5.1? Thanks, Ehud Schreiber. -- 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] Protein stability using MARTINI
Thanks Mark for the replay, I used VDW presentation to over come it. Best, Itamar On 6/09/2010 6:33 PM, Mark Abraham wrote: - Original Message - From: Itamar Kass Date: Monday, September 6, 2010 14:06 Subject: [gmx-users] Protein stability using MARTINI To: Discussion list for GROMACS users > HI all, > > I am simulating a protein in water using the MARTINI (CG) force > field. My protein composed of few alpha-helices and a big tail > (~50AA) which is random coiled. I have built the simulation > system according to the procedure at > http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in- > water . > > After a 10ns simulation, I have visualised the system using VMD. > It seems like the protein had dismantled to amino acids. I see > groups of bids moving freely in the system. I'm not sure what you mean here, but it seems likely that VMD's heuristics for guessing where bonds between atoms might exist aren't going to work well for a coarse-grained protein. There's probably a standard solution, for which you should Google :-) Mark > > Any idea of the problem? Any idea how to fix it? > > PS I don't want to use elastic network for the random coil tail, > as I wish to capture as much conformation as possible. > > Thanks in advance, > Itamar. > > -- > > > "In theory, there is no difference between theory and practice. > But, in practice, there is." - Jan L.A. van de Snepscheut > > === > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu > > > -- > 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 -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] Protein stability using MARTINI
Dear Itamar, If your problem is not a bond length definition in VMD (which you can overcome by using "dynamic bonds", although it is not perfect) you may have a problem in your topology. The way you describe your problem (groups of bids moving freely) suggests that you do have a topology problem. XAvier. On Sep 6, 2010, at 11:52 AM, Itamar Kass wrote: Thanks Mark for the replay, I used VDW presentation to over come it. Best, Itamar On 6/09/2010 6:33 PM, Mark Abraham wrote: - Original Message - From: Itamar Kass Date: Monday, September 6, 2010 14:06 Subject: [gmx-users] Protein stability using MARTINI To: Discussion list for GROMACS users > HI all, > > I am simulating a protein in water using the MARTINI (CG) force > field. My protein composed of few alpha-helices and a big tail > (~50AA) which is random coiled. I have built the simulation > system according to the procedure at > http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in- > water . > > After a 10ns simulation, I have visualised the system using VMD. > It seems like the protein had dismantled to amino acids. I see > groups of bids moving freely in the system. I'm not sure what you mean here, but it seems likely that VMD's heuristics for guessing where bonds between atoms might exist aren't going to work well for a coarse-grained protein. There's probably a standard solution, for which you should Google :-) Mark > > Any idea of the problem? Any idea how to fix it? > > PS I don't want to use elastic network for the random coil tail, > as I wish to capture as much conformation as possible. > > Thanks in advance, > Itamar. > > -- > > > "In theory, there is no difference between theory and practice. > But, in practice, there is." - Jan L.A. van de Snepscheut > > === > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu > > > -- > 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 -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] the broken of the molecules
Hi, If you are using PBC, mdrun will sometimes write sets of coordinates such that molecules appear "broken" across periodic boundaries. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for solution approaches. Linear species can sometimes have other problems, which have been discussed on the mailing list before. Mark - Original Message - From: kecy...@sina.com Date: Monday, September 6, 2010 18:43 Subject: [gmx-users] the broken of the molecules To: gmx-users > Hello, I do the energy minimization of the butylene box , but some butylene > molecules are broken after that. The butylene itp file is produced by PRODRG, > as follows: > > [ moleculetype ] > ; Name nrexcl > BUT 3 > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 CH3 1 BUT C9 10.0049 15.0350 > 2 CH2 1 BUT C6 1 -0.02442 14.0270 > 3 C 1 BUT C3 10.07957 13.0190 > 4 C 1 BUT C2 1 -0.06005 14.0270 > [ bonds ] > ; ai aj fuc0, c1, ... >2 1 20.155 715.00.155 715.0 ;C6 C9 >2 3 20.153 715.00.153 715.0 ;C6 C3 >3 4 20.135 715.00.135 715.0 ;C3 C2 > [ pairs ] > ; ai aj fuc0, c1, ... >1 4 1 ;C9 C2 > [ angles ] > ; ai aj ak fuc0, c1, ... >1 2 3 2112.5 520.0112.5 520.0 ;C9 C6 C3 > >2 3 4 2125.0 610.0125.0 610.0 ;C6 C3 C2 > > [ dihedrals ] > ; ai aj ak al fuc0, c1, m, ... >1 2 3 4 1 0.01.0 6 0.01.0 6 ; dihC9 C6 > C3 C2 > > Can you show me why the butylene molecules would be broken? > Thank you very much ! > > -- > 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] Protein stability using MARTINI
Hey, It might also be related to the PBC, with gromacs not writing whole molecules anymore. Maybe a link to a picture would be good, showing protein beads spheres, together with the (triclinic) unit cell. Cheers, Tsjerk On Mon, Sep 6, 2010 at 12:05 PM, XAvier Periole wrote: > > Dear Itamar, > If your problem is not a bond length definition in VMD (which > you can overcome by using "dynamic bonds", although it is not > perfect) you may have a problem in your topology. > The way you describe your problem (groups of bids moving freely) > suggests that you do have a topology problem. > XAvier. > On Sep 6, 2010, at 11:52 AM, Itamar Kass wrote: > > Thanks Mark for the replay, > I used VDW presentation to over come it. > Best, > Itamar > > On 6/09/2010 6:33 PM, Mark Abraham wrote: > > - Original Message - > From: Itamar Kass > Date: Monday, September 6, 2010 14:06 > Subject: [gmx-users] Protein stability using MARTINI > To: Discussion list for GROMACS users > >> HI all, >> >> I am simulating a protein in water using the MARTINI (CG) force >> field. My protein composed of few alpha-helices and a big tail >> (~50AA) which is random coiled. I have built the simulation >> system according to the procedure at >> http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in- >> water . >> >> After a 10ns simulation, I have visualised the system using VMD. >> It seems like the protein had dismantled to amino acids. I see >> groups of bids moving freely in the system. > > I'm not sure what you mean here, but it seems likely that VMD's heuristics > for guessing where bonds between atoms might exist aren't going to work well > for a coarse-grained protein. There's probably a standard solution, for > which you should Google :-) > > Mark > >> >> Any idea of the problem? Any idea how to fix it? >> >> PS I don't want to use elastic network for the random coil tail, >> as I wish to capture as much conformation as possible. >> >> Thanks in advance, >> Itamar. >> >> -- >> >> >> "In theory, there is no difference between theory and practice. >> But, in practice, there is." - Jan L.A. van de Snepscheut >> >> === >> | Itamar Kass, Ph.D. >> | Postdoctoral Research Fellow >> | >> | Department of Biochemistry and Molecular Biology >> | Building 77 Clayton Campus >> | Wellington Road >> | Monash University, >> | Victoria 3800 >> | Australia >> | >> | Tel: +61 3 9902 9376 >> | Fax: +61 3 9902 9500 >> | E-mail: itamar.k...@monash.edu >> >> >> -- >> gmx-users mailing list gmx-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 > > -- > > > "In theory, there is no difference between theory and practice. But, in > practice, there is." - Jan L.A. van de Snepscheut > > === > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu > > > -- > gmx-users mailing list gmx-us...@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 list gmx-us...@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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- 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] PMF
Hi All I have generated a potential of mean force curve for two cage molecules. The profile of the curve is very good apart from the fact that the repulsive part of the curve doesn't go above zero. My attractive tail therefore appears higher than the repulsive part. The histograms are very well behaved. I use a force constant of 1000 for all sampling windows. At closer distances between the centres of mass (the repulsive part), the mean value is not centred around the ref distance, I assume due to repulsion. To circumvent this I have increased the force constant to 1 for the last sample distance. My PMF curve has now a constant value of zero even though the histograms are fine. Why is this so ? Cheers Gavin -- 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] grompp_d and mdrun_d issues with GBSA and normal mode analysis
Hi! This should work. I checked the code but did not find anything obvious. Could you please file a bugzilla and I'll have a look as soon as possible. Thanks! /Per 6 sep 2010 kl. 11.38 skrev Ehud Schreiber: > Dear GROMACS users, > > I am encountering a couple of issues when trying to perform normal mode > analysis in an implicit solvent (GBSA) setting. > I am using version 4.5.1 with double precision; unfortunately I do not have > the single precision version installed for comparison. > > The starting point is a small protein which was energy minimized in two > stages, also in double precision and with GBSA, producing “em2” files. The > mdp file used for the normal mode analysis is the following: > > - nm.mdp - > integrator = nm > nsteps = 1 > implicit_solvent = GBSA > gb_algorithm = Still ; the default > rgbradii = 1.0 ; must be equal to rlist > rlist= 1.0 > coulombtype = cut-off > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.0 > --- > > The command used is > > grompp_d -f nm.mdp -p topol.top -c em2.gro -t em2.trr -o nm.tpr > > which ran fine except for the following note: > > NOTE 1 [file nm.mdp]: > You are using a plain Coulomb cut-off, which might produce artifacts. > You might want to consider using PME electrostatics. > > Then, I tried to run > > mdrun_d -v -nice 0 -deffnm nm > > However, the command seems to be stuck, and the following serious warning is > produced: > > Warning: 1-4 interaction between 64 and 71 at distance 3.114 which is larger > than the 1-4 table size 2.000 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > Maximum force: 3.48709e+06 > Maximum force probably not small enough to ensure that you are in an > energy well. Be aware that negative eigenvalues may occur when the > resulting matrix is diagonalized. > > The em2.gro is definitely not having such a large distance between atoms 64 > and 71: > > 6GLN CB 64 1.879 1.895 2.423 > . > . > 6GLNOE1 71 2.047 1.715 2.642 > > which are only about 0.346 nm apart. Also, the energy minimization, which > used the same options, mutatis mutandis, > > -- em2.mdp -- > integrator = cg > nsteps = 1000 > nstcgsteep = 40 > implicit_solvent = GBSA > gb_algorithm = Still ; the default > rgbradii = 1.0 ; must be equal to rlist > nstlist = 10 > rlist= 1.0 > coulombtype = cut-off > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.0 > nstenergy= 10 > - > > converged to machine precision having a much smaller maximum force: > > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 10 > > Polak-Ribiere Conjugate Gradients converged to machine precision in 0 steps, > but did not reach the requested Fmax < 10. > Potential Energy = -2.71868395521758e+04 > Maximum force = 4.63436548427712e+02 on atom 584 > Norm of force = 1.25296847735530e+02 > > The other problem arises when I try to follow the grompp_d note above and > change in nm.mdp to > > coulombtype = pme > > I then have a fatal error: > > ERROR 1 [file nm.mdp]: > With GBSA, coulombtype must be equal to Cut-off > > Am I doing something wrong or are there still some problems in the new GBSA > option of version 4.5.1? > > Thanks, > Ehud Schreiber. > > -- > 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] g_covar & g_anaeig problems
Hey everyone, searching the list for the answer to a g_covar problem I've found this post of Arne who describes the very same problem that I encounter. I'm observing this problem on a linux cluster with 32GB memory on each node. The g_covar_d application was compiled in double precision with an intel compiler and works fine up to a number of atoms of around 15408. In tests I could find out that above this number +/- 48 atoms I receive the following error output: Calculating the average structure ... Last frame 50 time 5000.000 Constructing covariance matrix (46368x46368) ... Reading frame 0 time0.000 Segmentation fault Meaning a matrix over around 46224x46224 elements starts to generate this problem. Did anyone encounter the same problem or does anyone has a hint to solve this issue? Kind regards Sebastian Am 25.03.2010 10:05, schrieb arne.wag...@student.uib.no: Hi everyone, I've got the following two problems - hopefully someone can help me fixing them. 1.: I have a larger system ~2 atoms where I performed an MD run and now I want to analyze the entropy. I tried a combination of g_covar and g_anaeig to get the values. Input: g_covar -f XXX_md_eq.xtc -n XXX.ndx -s XXX_md_eq.tpr -v XXX_eivec.trr -mwa -l XXX_covar.log If I choose a larger sub-part of the system (approx. > 4000 elements) I get the following error message after the average structure is calculated: Constructing covariance matrix ... Reading frame 0 time0.000 Segmentation fault Is this a result of insufficient memory or is there an error in the whole procedure? 2.: In smaller sub-parts I can get the eigenvectors and when I put them into g_anaeig, g_anaeig -v XXX.trr -entropy I get values for the quasi-harmonical-approximation but an 'inf' oder 'nan' for the Schlitter entropy calculation - even with additional/maximum input. Why? Thanks a lot! Awa -- _ Sebastian Breuers Tel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für Chemie Department of Chemistry Organische Chemie Organic Chemistry Greinstraße 4 Greinstraße 4 D-50939 KölnD-50939 Cologne, Federal Rep. of Germany _ -- 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] Problems with CMake and shared libraries
Hi All, I've discovered a new problem when using CMake. To recap, the system in question is a PowerPC cluster running Yellowdog Linux with OpenMPI-1.4.2 and gcc-4.2.2, linking against FFTW 3.0.1. I gave the following commands to build mdrun with CMake: cmake ../gromacs-4.5.1 -DFFTW3F_LIBRARIES=/home/rdiv1001/fftw-3.0.1-linux/lib/libfftw3f.so -DFFTW3F_INCLUDE_DIR=/home/rdiv1001/fftw-3.0.1-linux/include/ -DCMAKE_INSTALL_PREFIX=/home/rdiv1001/gromacs-4.5_cmake-linux -DGMX_BINARY_SUFFIX=_4.5_cmake_mpi –DGMX_THREADS=OFF –DGMX_X11=OFF -DGMX_MPI=ON -DMPI_COMPILER=/home/rdiv1001/compilers/openmpi-1.4.2/bin/mpicxx -DMPI_INCLUDE_PATH=/home/rdiv1001/compilers/openmpi-1.4.2/include make mdrun make install-mdrun When attempting to invoke the resulting "mdrun_4.5.1_cmake_mpi" executable, I get the following error: /home/rdiv1001/gromacs-4.5.1_cmake-linux/bin/mdrun_4.5.1_cmake_mpi: error while loading shared libraries: libgmxpreprocess_mpi.so.6: cannot open shared object file: No such file or directory Adding -DBUILD_SHARED_LIBS=OFF solves the problem. Since (by default) Gromacs builds shared libraries, I thought this little problem should be reported, even though I can work around it. The cmake and subsequent make steps reported no problems whatsoever beyond a couple of minor compiler warnings, so I assumed that everything had gone well. -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/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] ffamber03 H0 atomtype in 4.5.1
Hello Gromacs users, I have recently set up some simulations of a peptide using the amber03 force field in 4.5.1 and implicit solvent. When I run it through grompp, it gives me the following: --- Program grompp-4.5.1, VERSION 4.5.1 Source code file: grompp.c, line: 870 Fatal error: Can't do GB electrostatics; the forcefield is missing 1 values for atomtype radii, or they might be negative . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The missing value it is referring to was also mentioned in the grompp output: *** GB parameter(s) missing or negative for atom type 'H0' *** The 'H0' (read h-zero) atomtype only appears in glycine residues. It is equivalent in all ways to the 'H1' (read h-one) atomtype. But for some reason, in the gbsa.itp file, the 'H0' atomtype is commented out. When it is un-commented, grompp proceeds as normal. My question is why is this specific atomtype commented out in the amber03 gbsa.itp file? Thanks in advance, Joe -- 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] ffamber03 H0 atomtype in 4.5.1
Hi! This seems to be an unfortunate mistake. It should not be commented out. Thank you for reporting this, I will fix it for the next release. Cheers /Per 6 sep 2010 kl. 17.08 skrev William Joseph Allen: > Hello Gromacs users, > > I have recently set up some simulations of a peptide using the amber03 force > field in 4.5.1 and implicit solvent. When I run it through grompp, it gives > me the following: > > --- > Program grompp-4.5.1, VERSION 4.5.1 > Source code file: grompp.c, line: 870 > > Fatal error: > Can't do GB electrostatics; the forcefield is missing 1 values for > atomtype radii, or they might be negative > . > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > The missing value it is referring to was also mentioned in the grompp output: > > *** > GB parameter(s) missing or negative for atom type 'H0' > *** > > The 'H0' (read h-zero) atomtype only appears in glycine residues. It is > equivalent in all ways to the 'H1' (read h-one) atomtype. But for some > reason, in the gbsa.itp file, the 'H0' atomtype is commented out. When it is > un-commented, grompp proceeds as normal. My question is why is this specific > atomtype commented out in the amber03 gbsa.itp file? > > Thanks in advance, > > Joe > -- > 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] Problems with CMake and shared libraries
Hi, Indeed, the custom cmake target "install-mdrun" was designed to only install the mdrun binary and it does not install the libraries this is linked against when BUILD_SHARED_LIBS=ON. I'm not completely sure that this is actually a bug, but to me it smells like one. I'll file a bug report and will sort this issue out. Thanks Justin for reporting! Cheers, -- Szilárd On Mon, Sep 6, 2010 at 5:37 PM, Justin A. Lemkul wrote: > > Hi All, > > I've discovered a new problem when using CMake. To recap, the system in > question is a PowerPC cluster running Yellowdog Linux with OpenMPI-1.4.2 and > gcc-4.2.2, linking against FFTW 3.0.1. > > I gave the following commands to build mdrun with CMake: > > cmake ../gromacs-4.5.1 > -DFFTW3F_LIBRARIES=/home/rdiv1001/fftw-3.0.1-linux/lib/libfftw3f.so > -DFFTW3F_INCLUDE_DIR=/home/rdiv1001/fftw-3.0.1-linux/include/ > -DCMAKE_INSTALL_PREFIX=/home/rdiv1001/gromacs-4.5_cmake-linux > -DGMX_BINARY_SUFFIX=_4.5_cmake_mpi –DGMX_THREADS=OFF –DGMX_X11=OFF > -DGMX_MPI=ON > -DMPI_COMPILER=/home/rdiv1001/compilers/openmpi-1.4.2/bin/mpicxx > -DMPI_INCLUDE_PATH=/home/rdiv1001/compilers/openmpi-1.4.2/include > > make mdrun > > make install-mdrun > > When attempting to invoke the resulting "mdrun_4.5.1_cmake_mpi" executable, > I > get the following error: > > /home/rdiv1001/gromacs-4.5.1_cmake-linux/bin/mdrun_4.5.1_cmake_mpi: error > while > loading shared libraries: libgmxpreprocess_mpi.so.6: cannot open shared > object > file: No such file or directory > > Adding -DBUILD_SHARED_LIBS=OFF solves the problem. Since (by default) > Gromacs > builds shared libraries, I thought this little problem should be reported, > even > though I can work around it. The cmake and subsequent make steps reported > no > problems whatsoever beyond a couple of minor compiler warnings, so I assumed > that everything had gone well. > > -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 list gmx-us...@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] pdb2gmx -chainsep vs -merge
Dear Gromacs Users, Has anybody merged all chains in a PDB file using -chainsep. because -chainsep does not seem to work. http://www.mail-archive.com/gmx-users@gromacs.org/msg33192.html Is there a alternate way of doing it ?, One way I could think of is to add the atoms numbers in the topologies. would appreciate better ideas.. Best, nahren -- 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] pdb2gmx -chainsep vs -merge
nahren manuel wrote: Dear Gromacs Users, Has anybody merged all chains in a PDB file using -chainsep. because -chainsep does not seem to work. http://www.mail-archive.com/gmx-users@gromacs.org/msg33192.html Is there a alternate way of doing it ?, One way I could think of is to add the atoms numbers in the topologies. would appreciate better ideas.. If pdb2gmx -merge suits your needs then just generate the topology with an earlier version. -Justin Best, nahren -- 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] about rdf
Hello, 1- In the manual I see rdf plot for Oxygen-Oxygen of SPC-water. I think this shows the average O-O density between all water molecules. I read a post saying that rdf is calculating C_C distances for each C on chain 1 for instance and all other C on the chain and other chains.. http://lists.gromacs.org/pipermail/gmx-users/2006-November/024831.html Now I am trying to do the same thing to get rdf for C-C or C-H for polymer chains. I looked into default index groups and I guess Protein-H, BAckbone and Mainchain groups for my system should give only carbon atoms (I have only polyethylene chains), and Non-Protein should give only H. but I do not know how I can use them since System is the only default group I see. 2- What doesy axis show? the average number density? ( I am calculating rdf between chains 1 and 2 for instance. y-axis is in the range of 0-300 ?! and x-axis varies between 0-15 nm?!. normally g(r) is in the range of 1 to 5 ..). and also I noticed it takes much time for the program to read all frames when I issue the command below even for only 2 chains having 60 ethylene units. Am I doing something wrong? g_rdf -f *.trr -s *.tpr -o rdf -n *.ndx Group 0 ( System) has 2896 elements Group 1 ( PE60-1) has 362 elements Group 2 ( PE60-2) has 362 elements Group 3 ( PE60-3) has 362 elements Group 4 ( PE60-4) has 362 elements Group 5 ( PE60-5) has 362 elements Group 6 ( PE60-6) has 362 elements Group 7 ( PE60-7) has 362 elements Group 8 ( PE60-8) has 362 elements groups 1 to 8 each contain all C and H atoms in the molecule. Thanks, -- 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] about rdf
Moeed wrote: Hello, 1- In the manual I see rdf plot for Oxygen-Oxygen of SPC-water. I think this shows the average O-O density between all water molecules. I read a post saying that rdf is calculating C_C distances for each C on chain 1 for instance and all other C on the chain and other chains.. http://lists.gromacs.org/pipermail/gmx-users/2006-November/024831.html I don't see how you drew that conclusion from that post. g_rdf calculates probabilities based on all atomic pairs in the index group selection, unless -com is invoked, in which case the center of mass of the reference group is used. Now I am trying to do the same thing to get rdf for C-C or C-H for polymer chains. I looked into default index groups and I guess Protein-H, BAckbone and Mainchain groups for my system should give only carbon atoms (I have only polyethylene chains), and Non-Protein should give only H. but I do not know how I can use them since System is the only default group I see. Do you have protein molecules? If not, then you won't have default groups like Protein, Protein-H... 2- What doesy axis show? the average number density? ( I am calculating Please use Google to answer this question. rdf between chains 1 and 2 for instance. y-axis is in the range of 0-300 ?! and x-axis varies between 0-15 nm?!. normally g(r) is in the range of 1 to 5 ..). and also I noticed it takes much time for the program to Normally? Based on what assessment? Unless you have exceptionally good sampling, your RDF plot probably won't converge very well for large molecules, especially if you are analyzing all possible atomic pairs. read all frames when I issue the command below even for only 2 chains having 60 ethylene units. Am I doing something wrong? No, but g_rdf is doing something on the order of 362*362 calculations, so you can count on that taking a lot of time (and memory). -Justin g_rdf -f *.trr -s *.tpr -o rdf -n *.ndx Group 0 ( System) has 2896 elements Group 1 ( PE60-1) has 362 elements Group 2 ( PE60-2) has 362 elements Group 3 ( PE60-3) has 362 elements Group 4 ( PE60-4) has 362 elements Group 5 ( PE60-5) has 362 elements Group 6 ( PE60-6) has 362 elements Group 7 ( PE60-7) has 362 elements Group 8 ( PE60-8) has 362 elements groups 1 to 8 each contain all C and H atoms in the molecule. Thanks, -- 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
Re: [gmx-users] pdb2gmx -chainsep vs -merge
- Original Message - From: nahren manuel Date: Tuesday, September 7, 2010 7:16 Subject: [gmx-users] pdb2gmx -chainsep vs -merge To: gromacs gromacs --- | > Dear Gromacs Users, > Has anybody merged all chains in a PDB file using -chainsep. because > -chainsep does not > seem to work. > > http://www.mail-archive.com/gmx-users@gromacs.org/msg33192.html > > Is there a alternate way of doing it ?, > One way I could think of is to add the atoms numbers in the topologies. One work-around for the -chainsep situation you've observed is to remove or rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when it tries to merge the chains. It should be taking care of that itself, but handling it yourself might help. pdb2gmx can probably rebuild the carboxyl oxygen. Keeping (one of the) OXT atoms and renaming it to "O" (keeping the fixed-column format correct) might be needed. 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_covar & g_anaeig problems
- Original Message - From: Sebastian Breuers Date: Tuesday, September 7, 2010 0:42 Subject: Re: [gmx-users] g_covar & g_anaeig problems To: gmx-users@gromacs.org > Hey everyone, > > searching the list for the answer to a g_covar problem I've > found this post of Arne who describes the very same problem that > I encounter. > > I'm observing this problem on a linux cluster with 32GB memory > on each node. The g_covar_d application was compiled in double > precision with an intel compiler and works fine up to a number > of atoms of around 15408. In tests I could find out that above > this number +/- 48 atoms I receive the following error output: > > > Calculating the average structure ... > Last frame 50 > time 5000.000 > > Constructing covariance matrix (46368x46368) ... > Reading frame 0 > time0.000 Segmentation fault > > Meaning a matrix over around 46224x46224 elements starts to > generate this problem. > > Did anyone encounter the same problem or does anyone has a hint > to solve this issue? Get more memory or use fewer atoms :-) The memory needs and run time will scale at least as high as the square of the number of atoms. Probably you can ignore at least your hydrogen atoms... 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
