Re: [gmx-users] trjcat error
Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error: --- Checking file PRO_DAH_10_NS.part0004.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 1.000 # Atoms 135496 Reading frame1400 time 12800.001 --- Program gmxcheck, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Is there any way to recover this .trr file? Or do I need to re-run the simulation again? Any suggestion is welcome. Regards, Anirban On Fri, Dec 18, 2009 at 12:49 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Anirban, Check each trajectory with gmxcheck to see whether they are okay. Cheers, Tsjerk On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to join them into a single .trr file for analysis and getting the following error: --- Continue writing frames from PRO_10_NS.part0003.trr t=4604 ps, frame=2302 - frame 3990 time 7980.000 ps - frame 3910 time 7820.000 ps --- Program trjcat, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file What should I do? Any suggestion is welcome. Regards, Anirban -- 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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] trjcat error
Anirban Ghosh wrote: Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error: --- Checking file PRO_DAH_10_NS.part0004.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 1.000 # Atoms 135496 Reading frame1400 time 12800.001 --- Program gmxcheck, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Is there any way to recover this .trr file? Or do I need to re-run the simulation again? Probably. Did the simulation end correctly? Did you run out of disk space? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjcat error
Thanks Mark for the reply. The simulation ran fine and at the end of the .log file I got the following line: - Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 125029.000 125029.000100.0 1d10h43:49 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:932.867 46.259 3.729 6.436 Finished mdrun on node 0 Fri Dec 11 22:58:06 2009 -- There was no error and I did not ran out of disk space. What should I do now? Can I repair this .trr file anyway? Any suggestion is welcome. Regards, Anirban On Fri, Dec 18, 2009 at 2:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Anirban Ghosh wrote: Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error: --- Checking file PRO_DAH_10_NS.part0004.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 1.000 # Atoms 135496 Reading frame1400 time 12800.001 --- Program gmxcheck, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Is there any way to recover this .trr file? Or do I need to re-run the simulation again? Probably. Did the simulation end correctly? Did you run out of disk space? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjcat error
Anirban Ghosh wrote: Thanks Mark for the reply. The simulation ran fine and at the end of the .log file I got the following line: - Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 125029.000 125029.000100.0 1d10h43:49 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:932.867 46.259 3.729 6.436 Finished mdrun on node 0 Fri Dec 11 22:58:06 2009 -- There was no error and I did not ran out of disk space. What should I do now? Can I repair this .trr file anyway? Any suggestion is welcome. Well if you haven't broken the file since (check its size), it was not written properly during the calculation. This sort of thing can happen with remote-mounted disks, etc. if the underlying filesystem is not solid. Mark On Fri, Dec 18, 2009 at 2:02 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Anirban Ghosh wrote: Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error: --- Checking file PRO_DAH_10_NS.part0004.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 1.000 # Atoms 135496 Reading frame1400 time 12800.001 --- Program gmxcheck, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Is there any way to recover this .trr file? Or do I need to re-run the simulation again? Probably. Did the simulation end correctly? Did you run out of disk space? Mark -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://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] reference for make_edi -linacc
Hello, does anybody have a reference for the -linacc method applied by make_edi/mdrun? I have checked the references mentioned in make_edi -h as well as the manual, but didn't find anything that matches -linacc exactly. For example, gromacs suggests that entire MD steps will be accepted or rejected if they do or do not move in the desired direction along the selected eigenvectors, respectively: -linacc: perform acceptance linear expansion along selected eigenvectors. (steps in the desired directions will be accepted, others will be rejected). While the published version appears to be more complex: B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; An extended sampling of the configurational space of HPr from E. coli PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996) Briefly, the algorithm consists of the following steps: a starting position is defined as the set of essential coordinates of the starting conformation; a number of regular MD steps is preformed; for each step, a new starting position is accepted only if it is not closer to the starting position than the previous position, in the subspace defined by the first three eigenvectors (i.e., if the distance from the starting position in this subspace does not decrease). If the new position is closet to the starting position, a correctio is applied only in the subspace defied by the first three eigenvectors with least perturbation. Thank you, Chris. -- 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] reference for make_edi -linacc
Hi Chris, Maybe in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303567/ Daidone et al., Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c Ran. chris.ne...@utoronto.ca wrote: Hello, does anybody have a reference for the -linacc method applied by make_edi/mdrun? I have checked the references mentioned in make_edi -h as well as the manual, but didn't find anything that matches -linacc exactly. For example, gromacs suggests that entire MD steps will be accepted or rejected if they do or do not move in the desired direction along the selected eigenvectors, respectively: -linacc: perform acceptance linear expansion along selected eigenvectors. (steps in the desired directions will be accepted, others will be rejected). While the published version appears to be more complex: B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; An extended sampling of the configurational space of HPr from E. coli PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996) Briefly, the algorithm consists of the following steps: a starting position is defined as the set of essential coordinates of the starting conformation; a number of regular MD steps is preformed; for each step, a new starting position is accepted only if it is not closer to the starting position than the previous position, in the subspace defined by the first three eigenvectors (i.e., if the distance from the starting position in this subspace does not decrease). If the new position is closet to the starting position, a correctio is applied only in the subspace defied by the first three eigenvectors with least perturbation. Thank you, Chris. --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 thewww 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] reference for make_edi -linacc
Than you Ran, this looks good. The method is basically the same with the exception that Daidone et al. utilize a target structure as opposed to a target eigenvector, although the difference here is probably semantic. I greatly appreciate it, Chris. -- original message -- Hi Chris, Maybe in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303567/ Daidone et al., Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c Ran. chris.neale at utoronto.ca wrote: Hello, does anybody have a reference for the -linacc method applied by make_edi/mdrun? I have checked the references mentioned in make_edi -h as well as the manual, but didn't find anything that matches -linacc exactly. For example, gromacs suggests that entire MD steps will be accepted or rejected if they do or do not move in the desired direction along the selected eigenvectors, respectively: -linacc: perform acceptance linear expansion along selected eigenvectors. (steps in the desired directions will be accepted, others will be rejected). While the published version appears to be more complex: B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; An extended sampling of the configurational space of HPr from E. coli PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996) Briefly, the algorithm consists of the following steps: a starting position is defined as the set of essential coordinates of the starting conformation; a number of regular MD steps is preformed; for each step, a new starting position is accepted only if it is not closer to the starting position than the previous position, in the subspace defined by the first three eigenvectors (i.e., if the distance from the starting position in this subspace does not decrease). If the new position is closet to the starting position, a correctio is applied only in the subspace defied by the first three eigenvectors with least perturbation. Thank you, Chris. -- 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 -merge non interactive
Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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 intel I7 (2.67 GHz)
Dears, we have been trying to run gmx-4.0.X on new machines with the Intel I7 CPUs. It is a quad core intel on which multi-threading is a default feature. This makes the system to behave as a 8 cores machine. We observed some strange behavior of gromacs. Note that is certainly not due to gromacs itself. Running jobs using 4 cores we have observed the following behavior: - the info on the output files (log, xtc, edr ...) is not always printed - gromacs switches cores, eg: cores 1,2,4,5, and then 2,3,5,6 ... and this with no apparent logic. Jobs using 8 cores become extremely slow, more than expected, and if running at all. Running 2 jobs with 4 cores each, one was running with 4 cores, the second was using only 2 cores although mpirun was asked to use 4. This is more disturbing since it was also possible to run two jobs using 4 cores each successfully and have effectively increased efficiency: each job running at 5/6 of the speed of one run on 4 cores and running alone. This was observed with: - Ubuntu-9.10 (karmic) / kernel linux 2.6.31-14-generic (GNOME 2.28.1) - openmpi-1.3.2/1.4.X - gromacs 4.0.5/4.0.7 Anyone has any idea what could be going on on those I7? Thanks, We: Djurre ( XAvier) -- 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 -merge non interactive
Can't you just do one of these: echo 5 | pdb2gmx -f a.gro or pdb2gmx -f a.gro EOF 5 EOF --original message-- Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André -- 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] reference for make_edi -linacc
Hi Chris, I think linacc never rejects steps (the make_edi help is not quite correct here I am afraid) but either accepts them if they go into the right direction or otherwise corrects them. This way the system will without stalling go into the desired direction with respect to the selected eigenvector. From a quick look on the paper I assume that they are using the radacc method there. Carsten On Dec 18, 2009, at 4:48 PM, chris.ne...@utoronto.ca wrote: Hello, does anybody have a reference for the -linacc method applied by make_edi/mdrun? I have checked the references mentioned in make_edi -h as well as the manual, but didn't find anything that matches -linacc exactly. For example, gromacs suggests that entire MD steps will be accepted or rejected if they do or do not move in the desired direction along the selected eigenvectors, respectively: -linacc: perform acceptance linear expansion along selected eigenvectors. (steps in the desired directions will be accepted, others will be rejected). While the published version appears to be more complex: B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; An extended sampling of the configurational space of HPr from E. coli PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996) Briefly, the algorithm consists of the following steps: a starting position is defined as the set of essential coordinates of the starting conformation; a number of regular MD steps is preformed; for each step, a new starting position is accepted only if it is not closer to the starting position than the previous position, in the subspace defined by the first three eigenvectors (i.e., if the distance from the starting position in this subspace does not decrease). If the new position is closet to the starting position, a correctio is applied only in the subspace defied by the first three eigenvectors with least perturbation. Thank you, Chris. -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] pdb2gmx -merge non interactive
Hi, thanks for your answer! I think this only refers to the -ff force field selection. I tried several scripting solutions to pass y to the pdb2gmx questions whether to do the merging or not. Maybe my wires are just crossed but i did not find any hint to get rid of this questions. Can't you just do one of these: echo 5 | pdb2gmx -f a.gro or pdb2gmx -f a.gro EOF 5 EOF --original message-- Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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 -merge non interactive
What exactly did you try? Something like this? pdb2gmx -f a.gro EOF 5 y EOF I have not done -merge myself, but I often pass in multiple 'command-line' arguments in a scripts, although it is necessary to run it through on the command line once to see what the order of arguments should be. I could be the one whose wrong as I have never done -merge, but then again I have never had a problem automating any of the gromacs tools and I don't see why this one should be any different. -- original message -- Hi, thanks for your answer! I think this only refers to the -ff force field selection. I tried several scripting solutions to pass y to the pdb2gmx questions whether to do the merging or not. Maybe my wires are just crossed but i did not find any hint to get rid of this questions. Can't you just do one of these: echo 5 | pdb2gmx -f a.gro or pdb2gmx -f a.gro EOF 5 EOF --original message-- -- 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] error with changing pdb file
ksm tprk wrote: Hello Justin, I used ffgmx.n2t gromacs force field. and my topology file is: ; ; This is your include topology file ; Generated by x2top ; ; Include forcefield parameters #include ffgmx.itp [ moleculetype ] ; Namenrexcl ICE 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 C 1UNK C 0 0 12.011 C 0 0 ; qtot 0 2 C 1UNK C 1 0 12.011 C 0 0 ; qtot 0 3 C 1UNK C 2 . 24 C 1UNK C 23 0 12.011 C 0 0 ; qtot 0 25 N 1UNK N 24 014.0067 N 0 0 ; qtot 0 26 C 1UNK C 25 0 12.011 C 0 0 ; qtot 0 .. Thank you helping me, I can't keep trying to help you if you don't provide relevant information. If you want free help, you have to make it easy for those trying to help you. This topology snippet is not at all what I asked to see. To be clear, please post the following information: 1. The lines from the topology specified in the grompp error messages (the line numbers are given in the error messages) 2. The coordinate file entries that correspond to the atoms on those lines. It would be helpful to see the coordinate file that works, as well as the one that was modified that no longer works. Going back to your very first post, the root of the problem is that there are not bonded parameters in the ffgmx force field to describe whatever changes you made. Since you have yet to actually demonstrate what these changes were and how the affected the topology, there is no better help that anyone can provide. -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
Re: [gmx-users] pdb2gmx -merge non interactive
Hmm... although it is necessary to run it through on the command line once to see what the order of arguments should be ...exactly is the main problem as I don't know all the time how many chains are in the files I'm processing. Pdb2gmx asks for every chain included in your files. Though I can assume 8 chains in 99% of the files, I wanted to know if there may be a switch included in pdb2gmx like -ff. Maybe I prescan my files to get the amount of chains and then pass that value to my pdb2gmx script. Anyway, thanks for your answer, I appreciate it! What exactly did you try? Something like this? pdb2gmx -f a.gro EOF 5 y EOF I have not done -merge myself, but I often pass in multiple 'command-line' arguments in a scripts, although it is necessary to run it through on the command line once to see what the order of arguments should be. I could be the one whose wrong as I have never done -merge, but then again I have never had a problem automating any of the gromacs tools and I don't see why this one should be any different. -- original message -- Hi, thanks for your answer! I think this only refers to the -ff force field selection. I tried several scripting solutions to pass y to the pdb2gmx questions whether to do the merging or not. Maybe my wires are just crossed but i did not find any hint to get rid of this questions. Can't you just do one of these: echo 5 | pdb2gmx -f a.gro or pdb2gmx -f a.gro EOF 5 EOF --original message-- -- 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 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] pdb2gmx -merge non interactive
Hallo André, Check the wiki: http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive Oliver On Fri, Dec 18, 2009 at 10:59, Wojtyczka, André a.wojtyc...@fz-juelich.de wrote: Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André -- 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] error with changing pdb file
ksm tprk wrote: Hi Justin, I will try to be more clear. What I did, first I created a carbon nanotube using Tubegen carbon nanotube generator. After that I changed one carbon atom with another atom using text editor. My ffgmx file is same as what http://cs86.com/CNSE/SWNT.htm has. Next I created .top by applying ffgmx.n2t force field and .gro file respectively. And I used grompp to run my simulation. And What I got the error is: OK, the problem is pretty straightforward now. You have a nitrogen atom within a CNT, and there are no suitable angle parameters for such a system. The atom type chosen is simply N, which (from the ffgmx.atp file) corresponds to a peptide nitrogen in an amide, which is not what is present in your system so this assignment is incorrect. Perhaps NR6 might be more appropriate? -Justin creating statusfile for 8 nodes... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling cpp... processing topology... Generated 1282 of the 1485 non-bonded parameter combinations WARNING 1 [file cnt80.top, line 11144]: No default Angle types, using zeroes WARNING 2 [file cnt80.top, line 11144]: No default Angle types for perturbed atoms, using normal values WARNING 3 [file cnt80.top, line 11145]: No default Angle types, using zeroes WARNING 4 [file cnt80.top, line 11145]: No default Angle types for perturbed atoms, using normal values WARNING 5 [file cnt80.top, line 11187]: No default Angle types, using zeroes WARNING 6 [file cnt80.top, line 11187]: No default Angle types for perturbed atoms, using normal values WARNING 7 [file cnt80.top, line 11189]: No default Angle types, using zeroes WARNING 8 [file cnt80.top, line 11189]: No default Angle types for perturbed atoms, using normal values WARNING 9 [file cnt80.top, line 11190]: No default Angle types, using zeroes WARNING 10 [file cnt80.top, line 11190]: No default Angle types for perturbed atoms, using normal values Cleaning up temporary file grompp5QOA9q --- Program grompp_mpi, VERSION 3.3.1 Source code file: fatal.c, line: 416 The error atom is 25th atom. and the error lines specified in topology file are( I underlined and made bold them): . [ angles ] ; aiajak functc0c1c2 c3 2 120 1 1 2 3 1 2 3 4 1 2 322 1 4 322 1 3 4 5 1 * 3 425 1* *5 425 1* * * 4 5 6 1 5 6 7 1 6 7 8 1 6 726 1 8 726 1 7 8 9 1 7 829 1 9 829 1 8 910 1 91011 1 101112 1 101130 1 121130 1 111213 1 111233 1 131233 1 121314 1 131415 1 141516 1 141534 1 161534 1 151617 1 151637 1 171637 1 161718 1 171819 1 181920 1 181938 1 201938 1 12019 1 12021 1 192021 1 202122 1 202140 1 222140 1 32221 1 32223 1 212223 1 222324 1 222342 1 242342 1 * 232425 1* 232445 1 *252445 1* *42524 1* 42526 1 242526 1 72625 1 . I attached topology and coordinate files too. I am sorry that I gave not enough information. Thank you, Kasim I can't keep trying to help you if you don't provide relevant information. If you want free help, you have to make it easy for those trying to help you. This topology snippet is not at all what I asked to see. To be clear, please post the following information: 1. The lines from the topology specified in the grompp error messages (the line numbers are given in the error messages) 2. The coordinate file entries that correspond to the atoms on those lines. It would be helpful to see the coordinate file that works, as well as the one that was modified that no longer works. Going back to your very first post, the root of the problem is that there are not bonded parameters in the ffgmx force field to describe whatever changes you made. Since you have yet to actually demonstrate what these changes were and how the affected the topology, there is no better help that anyone can provide. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
For a detailed description of how to set up protein simulation, I recomend you to read the Martini Tutorial on http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html there you will find step by step instructions along with some explanations of what you are actually doing. In this case you only want to build a water box around your protein. For that you will use editconf and a vdw distance of 0.19. Regards Cesar 2009/12/17 rasoul nasiri nasiri1...@gmail.com yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have contribution to the denaturation mechanism. My question is about vdwd in beads of water. Is it OK if I select distances of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to reconstruct the system in smaller vdw distance of the water beads for doing my purpose. and Which commands of Gromacs can do it? Best regards Rasoul On Thu, Dec 17, 2009 at 5:03 PM, César Ávila clav...@gmail.com wrote: I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. 2009/12/17 rasoul nasiri nasiri1...@gmail.com Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? Rasoul On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users 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 intel I7 (2.67 GHz)
Alexey Shvetsov wrote: On Пятница 18 декабря 2009 19:29:15 XAvier Periole wrote: Dears, we have been trying to run gmx-4.0.X on new machines with the Intel I7 CPUs. It is a quad core intel on which multi-threading is a default feature. This makes the system to behave as a 8 cores machine. We observed some strange behavior of gromacs. Note that is certainly not due to gromacs itself. Running jobs using 4 cores we have observed the following behavior: - the info on the output files (log, xtc, edr ...) is not always printed - gromacs switches cores, eg: cores 1,2,4,5, and then 2,3,5,6 ... and this with no apparent logic. Jobs using 8 cores become extremely slow, more than expected, and if running at all. Running 2 jobs with 4 cores each, one was running with 4 cores, the second was using only 2 cores although mpirun was asked to use 4. This is more disturbing since it was also possible to run two jobs using 4 cores each successfully and have effectively increased efficiency: each job running at 5/6 of the speed of one run on 4 cores and running alone. This was observed with: - Ubuntu-9.10 (karmic) / kernel linux 2.6.31-14-generic (GNOME 2.28.1) - openmpi-1.3.2/1.4.X - gromacs 4.0.5/4.0.7 Anyone has any idea what could be going on on those I7? Thanks, We: Djurre ( XAvier) Well its usual behavior of systems with HT (Hyper threading) enabled. so its better to disable HT on such cpus so any cpu eating application like gromacs will run faster on it. No, this is not what I have heard from Berk Hess, he said that running 8 processes on 4 cores gives a speed up of 6-7 times a single core. It sounds more like you need to tune the kernel such that jobs stay on the core they are on. As far as I know Ubuntu is a Desktop OS, maybe you want a Server OS? -- 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://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] How can I reconstruct the system in CGMD simulation?
Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html . Is there difference between them? Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. Cheers Rasoul On Fri, Dec 18, 2009 at 9:02 PM, César Ávila clav...@gmail.com wrote: For a detailed description of how to set up protein simulation, I recommend you to read the Martini Tutorial on http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html there you will find step by step instructions along with some explanations of what you are actually doing. In this case you only want to build a water box around your protein. For that you will use editconf and a vdw distance of 0.19. Regards Cesar 2009/12/17 rasoul nasiri nasiri1...@gmail.com yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have contribution to the denaturation mechanism. My question is about vdwd in beads of water. Is it OK if I select distances of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to reconstruct the system in smaller vdw distance of the water beads for doing my purpose. and Which commands of Gromacs can do it? Best regards Rasoul On Thu, Dec 17, 2009 at 5:03 PM, César Ávila clav...@gmail.com wrote: I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. 2009/12/17 rasoul nasiri nasiri1...@gmail.com Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? Rasoul On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] problems with intel I7 (2.67 GHz)
On Пятница 18 декабря 2009 23:47:34 David van der Spoel wrote: Alexey Shvetsov wrote: On Пятница 18 декабря 2009 19:29:15 XAvier Periole wrote: Dears, we have been trying to run gmx-4.0.X on new machines with the Intel I7 CPUs. It is a quad core intel on which multi-threading is a default feature. This makes the system to behave as a 8 cores machine. We observed some strange behavior of gromacs. Note that is certainly not due to gromacs itself. Running jobs using 4 cores we have observed the following behavior: - the info on the output files (log, xtc, edr ...) is not always printed - gromacs switches cores, eg: cores 1,2,4,5, and then 2,3,5,6 ... and this with no apparent logic. Jobs using 8 cores become extremely slow, more than expected, and if running at all. Running 2 jobs with 4 cores each, one was running with 4 cores, the second was using only 2 cores although mpirun was asked to use 4. This is more disturbing since it was also possible to run two jobs using 4 cores each successfully and have effectively increased efficiency: each job running at 5/6 of the speed of one run on 4 cores and running alone. This was observed with: - Ubuntu-9.10 (karmic) / kernel linux 2.6.31-14-generic (GNOME 2.28.1) - openmpi-1.3.2/1.4.X - gromacs 4.0.5/4.0.7 Anyone has any idea what could be going on on those I7? Thanks, We: Djurre ( XAvier) Well its usual behavior of systems with HT (Hyper threading) enabled. so its better to disable HT on such cpus so any cpu eating application like gromacs will run faster on it. No, this is not what I have heard from Berk Hess, he said that running 8 processes on 4 cores gives a speed up of 6-7 times a single core. It sounds more like you need to tune the kernel such that jobs stay on the core they are on. As far as I know Ubuntu is a Desktop OS, maybe you want a Server OS? In this case seems cpuaffinity was turned off for mpi apps. check that kernel has cpusets support ale...@xeon /misc/_Work/RecA/pca $ zgrep CPUSET /proc/config.gz CONFIG_CPUSETS=y CONFIG_PROC_PID_CPUSET=y And check that your openmpi compiled with support of cpusets -- Alexey 'Alexxy' Shvetsov Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru signature.asc Description: This is a digitally signed message part. -- 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] error with changing pdb file
ksm tprk wrote: Hi Justin, I got same error before. The solution is still the same. You have listed all of your carbon atom types as simply C which corresponds to a bare carbon (carbonyl, etc) and if you search in ffgmxbon.itp for an angle involving three of these atoms, you won't find any. Choose a suitable atom type for these atoms and look for available parameters in ffgmxbon.itp. -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] exclusive list of matching searches on the gmx-users list
Hello, does anybody know how to get an exclusive list of matching searches while searching the gromacs mailing list using the new search tool? I have tried: essential dynamics Address not mapped essential dynamics and Address not mapped essential dynamics AND Address not mapped essential dynamics Address not mapped essential dynamics Address not mapped and in both cases I get hundreds of results that are related to one or the other of the topics that I am searching but the top results have no bearing on what I am actually looking for (I didn't check all 200+ results). The previous mailing list search was exclusive in this way. For example, I can still use the old search tool: http://oldwww.gromacs.org/swish-e/search/search2.php and a search for: essential dynamics Address not mapped clearly indicates that there are no hits. I like the new feature that I can see some of the text from the matching posts, but I have run into this implied-OR functionality before in other searches on this list and it really is a lot harder to find relevant posts now. If this implicit-OR functionality can not be removed or worked around, perhaps we should note this and put a link to the old search engine on the main page... Thanks, Chris. -- 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] Residue interaction energy
Dear All, Is there a way to calculated the interaction energy of a single residue with its environment? I would like to compare two simulations with a W residue in an alternative rotameric position. Thank you in advance, Abel -- 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] Residue interaction energy
abelius wrote: Dear All, Is there a way to calculated the interaction energy of a single residue with its environment? I would like to compare two simulations with a W residue in an alternative rotameric position. Read in the manual about the energygrps .mdp keyword. -Justin Thank you in advance, Abel -- 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] essential dynamics mdrun with SD integrator yields segmentation fault
Hello, In my hands, mdrun throws a segfault when passing the -ei flag to mdrun and utilizing the sd integrator. I'll admit that I have only tried this with a single system. Nevertheless, using -linacc vs. -linfix makes no difference, neither does moving to constraints=none or parallel vs. serial mdrun. However, when I change sd to md, the run is fine. With sd and -ei, the segfault is immediate: $ mdrun -deffnm edi -nosum -dlb yes -npme -1 -cpt 30 -maxh 48 -cpi edi.cpt -ei testpositive.edi -eo testpositive.edo :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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 (-: Option Filename Type Description -sedi.tpr InputRun input file: tpr tpb tpa -oedi.trr Output Full precision trajectory: trr trj cpt -xedi.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpiedi.cpt Input, Opt! Checkpoint file -cpoedi.cpt Output, Opt. Checkpoint file -cedi.gro Output Structure file: gro g96 pdb -eedi.edr Output Energy file: edr ene -gedi.log Output Log file -dgdl edi.xvg Output, Opt. xvgr/xmgr file -field edi.xvg Output, Opt. xvgr/xmgr file -table edi.xvg Input, Opt. xvgr/xmgr file -tablep edi.xvg Input, Opt. xvgr/xmgr file -tableb edi.xvg Input, Opt. xvgr/xmgr file -rerun edi.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpiedi.xvg Output, Opt. xvgr/xmgr file -tpid edi.xvg Output, Opt. xvgr/xmgr file -ei testpositive.edi Input, Opt! ED sampling input -eo testpositive.edo Output, Opt! ED sampling output -jedi.gct Input, Opt. General coupling stuff -joedi.gct Output, Opt. General coupling stuff -ffout edi.xvg Output, Opt. xvgr/xmgr file -devout edi.xvg Output, Opt. xvgr/xmgr file -runav edi.xvg Output, Opt. xvgr/xmgr file -pxedi.xvg Output, Opt. xvgr/xmgr file -pfedi.xvg Output, Opt. xvgr/xmgr file -mtxedi.mtx Output, Opt. Hessian matrix -dnedi.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -deffnm string edi Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum yes Dynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -[no]sum bool no Sum the energies at every step -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 30 Checkpoint interval (minutes) -[no]append bool no Append to previous output files when continuing from checkpoint -[no]addpart bool yes Add the simulation part number to all output files when continuing from checkpoint -maxhreal 48 Terminate after 0.99 times this time (hours) -multi int0 Do multiple simulations in
