[gmx-users] Box-size: please reply
Dear users, While calculating the box dimensions during a simulation of 20ns I got some strange values of the averages - Command used: g_energy -f ener.edr -o box.xvg Output: Energy Average Err.Est. RMSD Tot-Drift --- Box-X0.006655391.4 0.219101 -4.28575 (nm) Box-Y0.006656061.4 0.219101 -4.28574 (nm) Box-Z0.00470607 1 0.154928 -3.03048 (nm) While the actual dimensions are 7.2, 7.2 and 5.1 respectively. I use Gromacs-4.5.3, and 4.5.4 version also gave the same error. But when the .xvg file is examined it does not show much of the error indicated here. I also checked whether the is any discontinuity in the .edr file using gmxcheck and there was data from 0 to 20ns with no such discontinuity. I am attaching the corresponding .xvg plot. I had a similar problem before, and I was asked to check using the new version. Which I did ad there was no difference. Meanwhile I calculated the average values using other tools which gave 7.2, 7.2 and 5.1 respectively. So What is the problem here. Kindly clarify the confusion. Thanking you With Regards M. Kavyashree attachment: Box.png-- 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] regarding xtc file
Dear all, When I use mdrun_d to generate NPT or NVT ensemble I am not getting the .xtc file(compressed trajectory file). Further if I use .trr file to see the trajectory using VMD it shows nothing. I gave following command during mdrun, mdrun_d -s *.tpr -x *.xtc -o *.trr -cpo *.cpt -e *.edr -c *.gro -n *.ndx Is there anything wrong in the above commands or atleast why I am not able to view the trajectory using .trr file. Please suggest me something. Thank you. Ravi Kumar Venkatraman -- 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] Box-size: please reply
This mail was answered already... Please pay attention. http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html Tsjerk On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, While calculating the box dimensions during a simulation of 20ns I got some strange values of the averages - Command used: g_energy -f ener.edr -o box.xvg Output: Energy Average Err.Est. RMSD Tot-Drift --- Box-X 0.00665539 1.4 0.219101 -4.28575 (nm) Box-Y 0.00665606 1.4 0.219101 -4.28574 (nm) Box-Z 0.00470607 1 0.154928 -3.03048 (nm) While the actual dimensions are 7.2, 7.2 and 5.1 respectively. I use Gromacs-4.5.3, and 4.5.4 version also gave the same error. But when the .xvg file is examined it does not show much of the error indicated here. I also checked whether the is any discontinuity in the .edr file using gmxcheck and there was data from 0 to 20ns with no such discontinuity. I am attaching the corresponding .xvg plot. I had a similar problem before, and I was asked to check using the new version. Which I did ad there was no difference. Meanwhile I calculated the average values using other tools which gave 7.2, 7.2 and 5.1 respectively. So What is the problem here. Kindly clarify the confusion. Thanking you With Regards M. Kavyashree -- 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/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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/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] regarding xtc file
On 17/08/2011 4:31 PM, Ravi Kumar Venkatraman wrote: Dear all, When I use mdrun_d to generate NPT or NVT ensemble I am not getting the .xtc file(compressed trajectory file). Further if I use .trr file to see the trajectory using VMD it shows nothing. I gave following command during mdrun, mdrun_d -s *.tpr -x *.xtc -o *.trr -cpo *.cpt -e *.edr -c *.gro -n *.ndx mdrun_d -deffnm name is rather more efficient. Is there anything wrong in the above commands or atleast why I am not able to view the trajectory using .trr file. You're probably not writing anything to these files. Consult the contents of your .mdp file in the context of manual section 7.3.8 Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] FEP charged molecule cuestion
Hi there, Could someone please share some ideas about the next situation?: I am trying to estimate the relative binding affinity of two small molecules to a protein. In the setup process, ions are added in the solvent to neutralize the system. Then as everybody suggest, the ligand partial charges should be decouple to zero. But my specific case, the small molecules are charged, that means that after turning off the ligand partial charges, the system will have a net charge (because the ions in the solvent). Turning off the ions charges does not solve the problem, because of the protein charges. The concrete question are: Should I continue to atom mutation step using PME in a non-neutral system? It would make sense to turn off the partial charges of the some atoms in the small molecule (just those that are going to be mutated)? Thanks in advance Marcelino -- 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] suggestion that mdrun should ensure npme the numberof processes
Hi, On Aug 17, 2011, at 1:24 AM, chris.ne...@utoronto.ca chris.ne...@utoronto.ca wrote: Currently, gromacs4.5.4 gives a segfault if one runs mpirun -np 8 mdrun_mpi -npme 120 with no warning of the source of the problem. Obviously npmennodes is a bad setup, but a check would be nice. cr-npmenodes is set in mdrun.c right after the command line args are passed, and in the code there is also a comment that npmennodes should not cause a problem at that point. However, if npmennodes, in init_domain_decomposition / dd_choose_grid / optimize_ncells the number of pp nodes = nnodes-npme turns out to be negative such that in factorize the memory allocation does not work. I would have filed a bug report, however the web page seems to be down at the moment. Best, Carsten 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] reference structure of g_rms
Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. Could someone tell me what cause the different and which choice is better? And my version is gromacs v4.0.5 Sincerely yours, Hsin-Lin -- 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] reference structure of g_rms
On 17/08/11, Hsin-Lin Chiang jian...@phys.sinica.edu.tw wrote: Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. I think they should give the same result. If not, then the mostly likely explanation is that you've not used the files the way you think you have. You need to be able to issue grompp -f md -c pr -o md g_rms -s md.tpr -f whatever g_rms -s pr.gro -f whatever and get different results for there to be some kind of problem. In any case, you need to provide copies of your command lines and the different result in order for us to see whether you or GROMACS has done something wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do something else with our time :-) Mark Could someone tell me what cause the different and which choice is better? And my version is gromacs v4.0.5 Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] cutoffs
Hi, is it possible to have different cutoffs for different interactions? Best regards Anja -- 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] Box-size: please reply
Sorry Sir, I did not get that mail from the forum. Thank you With Regards Kavya On Wed, Aug 17, 2011 at 12:11 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: This mail was answered already... Please pay attention. http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html Tsjerk On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, While calculating the box dimensions during a simulation of 20ns I got some strange values of the averages - Command used: g_energy -f ener.edr -o box.xvg Output: Energy Average Err.Est. RMSD Tot-Drift --- Box-X0.006655391.4 0.219101 -4.28575 (nm) Box-Y0.006656061.4 0.219101 -4.28574 (nm) Box-Z0.00470607 1 0.154928 -3.03048 (nm) While the actual dimensions are 7.2, 7.2 and 5.1 respectively. I use Gromacs-4.5.3, and 4.5.4 version also gave the same error. But when the .xvg file is examined it does not show much of the error indicated here. I also checked whether the is any discontinuity in the .edr file using gmxcheck and there was data from 0 to 20ns with no such discontinuity. I am attaching the corresponding .xvg plot. I had a similar problem before, and I was asked to check using the new version. Which I did ad there was no difference. Meanwhile I calculated the average values using other tools which gave 7.2, 7.2 and 5.1 respectively. So What is the problem here. Kindly clarify the confusion. Thanking you With Regards M. Kavyashree -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box-size: please reply
Sir, I checked gmxdump -e ener.edr as suggested, I found that there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5 when I calculated the average for these values using another tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave some different answer as mentioned before in both 4.5.3 and 4.5.4 versions. Sorry I sent the mail twice as I did not receive Dr. Mark's reply form the forum. Thank you With Regards Kavya On Wed, Aug 17, 2011 at 4:15 PM, Kavyashree M hmkv...@gmail.com wrote: Sorry Sir, I did not get that mail from the forum. Thank you With Regards Kavya On Wed, Aug 17, 2011 at 12:11 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: This mail was answered already... Please pay attention. http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html Tsjerk On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, While calculating the box dimensions during a simulation of 20ns I got some strange values of the averages - Command used: g_energy -f ener.edr -o box.xvg Output: Energy Average Err.Est. RMSD Tot-Drift --- Box-X0.006655391.4 0.219101 -4.28575 (nm) Box-Y0.006656061.4 0.219101 -4.28574 (nm) Box-Z0.00470607 1 0.154928 -3.03048 (nm) While the actual dimensions are 7.2, 7.2 and 5.1 respectively. I use Gromacs-4.5.3, and 4.5.4 version also gave the same error. But when the .xvg file is examined it does not show much of the error indicated here. I also checked whether the is any discontinuity in the .edr file using gmxcheck and there was data from 0 to 20ns with no such discontinuity. I am attaching the corresponding .xvg plot. I had a similar problem before, and I was asked to check using the new version. Which I did ad there was no difference. Meanwhile I calculated the average values using other tools which gave 7.2, 7.2 and 5.1 respectively. So What is the problem here. Kindly clarify the confusion. Thanking you With Regards M. Kavyashree -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] cutoffs
On 17/08/11, Anja Kuhnhold anja.kuhnh...@physik.uni-halle.de wrote: Hi, is it possible to have different cutoffs for different interactions? Depends what you mean by that. Check out chapter 3 of the manual... 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] Box-size: please reply
On 17/08/2011 9:13 PM, Kavyashree M wrote: Sir, I checked gmxdump -e ener.edr as suggested, I found that there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5 when I calculated the average for these values using another tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave some different answer as mentioned before in both 4.5.3 and 4.5.4 versions. Sorry I sent the mail twice as I did not receive Dr. Mark's reply form the forum. OK, that looks like a bug of some kind. Please file an issue at redmine.gromacs.org (the server is down at the moment) uploading your input and output files and I'll take a look at it. Thanks. Mark Thank you With Regards Kavya On Wed, Aug 17, 2011 at 4:15 PM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Sorry Sir, I did not get that mail from the forum. Thank you With Regards Kavya On Wed, Aug 17, 2011 at 12:11 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: This mail was answered already... Please pay attention. http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html Tsjerk On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, While calculating the box dimensions during a simulation of 20ns I got some strange values of the averages - Command used: g_energy -f ener.edr -o box.xvg Output: Energy Average Err.Est. RMSD Tot-Drift --- Box-X0.006655391.4 0.219101 -4.28575 (nm) Box-Y0.006656061.4 0.219101 -4.28574 (nm) Box-Z0.00470607 1 0.154928 -3.03048 (nm) While the actual dimensions are 7.2, 7.2 and 5.1 respectively. I use Gromacs-4.5.3, and 4.5.4 version also gave the same error. But when the .xvg file is examined it does not show much of the error indicated here. I also checked whether the is any discontinuity in the .edr file using gmxcheck and there was data from 0 to 20ns with no such discontinuity. I am attaching the corresponding .xvg plot. I had a similar problem before, and I was asked to check using the new version. Which I did ad there was no difference. Meanwhile I calculated the average values using other tools which gave 7.2, 7.2 and 5.1 respectively. So What is the problem here. Kindly clarify the confusion. Thanking you With Regards M. Kavyashree -- gmx-users mailing list gmx-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/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-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/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
Could be a system blowing up, or perhaps a mis-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried productive runs. Now, no matter what I did, it crashed after few ps's of free MD or during the PR runs. Few of the things I had tried are: 1. Running the simulations on different systems (OSX, linux or blue-gene). 2. Using single or double precision versions. 3. An equilibration stage, 1ns long with a time-step of 1fs, during which the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. 4. Running part of the equilibration stage as NVT and then switched to NPT. 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom. Finally I had moved back to 4.0.7 which worked like charm. I wonder if someone else had encounter something like this. Attached please find the mdp files I used. All the best, 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] reference structure of g_rms
Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. I think they should give the same result. If not, then the mostly likely explanation is that you've not used the files the way you think you have. You need to be able to issue grompp -f md -c pr -o md g_rms -s md.tpr -f whatever g_rms -s pr.gro -f whatever and get different results for there to be some kind of problem. In any case, you need to provide copies of your command lines and the different result in order for us to see whether you or GROMACS has done something wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do something else with our time :-) Mark Hi, I checked the result again The order of the different is less than 0.1 nm. So that means this different is caused by precision? Sincerely yours, Hsin-Lin -- 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] Re: Recommended parameters for NVE simulation of SPCE water
Dear Professor Shirts, Thank you so much. I really appreciate your time in responding to my post and providing advice. I will try your suggested parameters for reasonably good energy conservation, and I will let you know how it goes. Thanks again for your time. I will be in touch. Andrew -- Date: Wed, 10 Aug 2011 17:50:13 -0400 From: Michael Shirts michael.shi...@virginia.edu Subject: Re: [gmx-users] Recommended parameters for NVE simulation of SPCEwater 1. NOTE 1 above suggests that I use vdwtype = Shift. When I do this, do you recommend that I apply long range dispersion corrections for both energy and pressure, using DispCorr = EnerPres, or for only energy, using DispCorr = Ener? Typically, for various (non-NVE) calculations, I have been using DispCorr = no, but I am not sure if this is a good idea. Pages 97-98 of the Gromacs 4.5.4 manual seem to suggest that the energy correction due to DispCorr is small and usually only significant for free energy calculations (which I will not be doing here). As a rule of thumb, do you typically turn dispersion corrections off? For constant pressure simulations, or for reaching the constant pressure equilibrium simulation, you should definitely include a dispersion correction -- the density will be too large, and will be cutoff dependent. For constant volume simulations, the dispersion correction will be constant. It will thus NOT affect energy conservation, but WILL affect average potential energy and average total energy, significantly. 2. NOTE 2 above suggests that I use either coulombtype = PME-Switch or coulombtype = Reaction-Field-zero. Do you have any advice or recommendation? For pretty good energy conservation, I would suggest: rlist = 1.3 coulombtype = PME rcoulomb= 1.1 vdw-type= Switch rvdw-switch= 1.0 rvdw = 1.1 This should work quite well -- you might get some drift after 1-2 ns, but not much. I'm working on developing suggested PME parameters right now for highly quantitative work, but it's not quite ready yet. Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- 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] reference structure of g_rms
Hi Hsin-Lin, If you use a .tpr file, you perform a mass-weighted fit and analysis. A .gro file has no masses and thus the fit and analysis are performed non-mass weighted, which will give differences, depending on the selection for the analysis. Hope it helps, Tsjerk 2011/8/17 Hsin-Lin Chiang jian...@phys.sinica.edu.tw: Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. I think they should give the same result. If not, then the mostly likely explanation is that you've not used the files the way you think you have. You need to be able to issue grompp -f md -c pr -o md g_rms -s md.tpr -f whatever g_rms -s pr.gro -f whatever and get different results for there to be some kind of problem. In any case, you need to provide copies of your command lines and the different result in order for us to see whether you or GROMACS has done something wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do something else with our time :-) Mark Hi, I checked the result again The order of the different is less than 0.1 nm. So that means this different is caused by precision? Sincerely yours, Hsin-Lin -- 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/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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/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] Add ions in the MARTINI force field
Dear GROMACS users, I am facing a problem to add ions to my system using the MARTINI force field. I try to replace cg water for Q beads but when I do that I get problems with the topology. My question is: How to add ions to a CG MARTINI system? Can I do that with genion? Can you share your experience with me? Best Regards, Edroaldo -- 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] converting cpt between single and double precision
On 2011-08-16 08:16:52PM -0500, Mark Abraham wrote:
On 17/08/2011 6:13 AM, Peter C. Lai wrote:
Is there a way to convert between single and double precision cpt files so
I can use double precision grompp on it to change some parameters but still
keep state information for continuity?
Or can I just trjconv_d the last frame of the single precision trr and feed
that to grompp -t?
(A machine I am using for preprocessing only has double precision tools and
it would be difficult to have both versions installed.)
Any GROMACS tool can read any of its binary formats written in either
precision, and write only in the precision with which the tool was compiled.
The problem is that when I use a double precision grompp and -t a single
precision .cpt, I get notices that it is discarding state data due to the
precision mismatch.
This is on 4.5.4:
Will read whole trajectory
Velocities generated: ignoring velocities in input trajectory
Precision mismatch for state entry box, code precision is double, file
precision is float
Precision mismatch for state entry box-rel, code precision is double, file
precision is float
Precision mismatch for state entry box-v, code precision is double, file
precision is float
Precision mismatch for state entry pres_prev, code precision is double, file
precision is float
Precision mismatch for state entry x, code precision is double, file precision
is float
Precision mismatch for state entry v, code precision is double, file precision
is float
the gmxdump of the resuling tpr confirms this:
boxv (3x3):
boxv[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev (3x3):
pres_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev (3x3):
svir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev (3x3):
fvir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
nosehoover_xi: not available
Interestingly enough, box and box_rel are preserved, despite the messages
to the contrary, but of course, the majority of the reason to use .cpt
is to transfer the velocities and virial...
--
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst | BEC 257
Genetics, Div. of Research | 1150 10th Avenue South
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808 |
==
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[gmx-users] Velocity of atom
Hello, How can I print/calculate on velocity of a atom. I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] reference structure of g_rms
Hi Tsjerk, It's very helpful information. Thank you very much Sincerely yours, Hsin-Lin Hi Hsin-Lin, If you use a .tpr file, you perform a mass-weighted fit and analysis. A .gro file has no masses and thus the fit and analysis are performed non-mass weighted, which will give differences, depending on the selection for the analysis. Hope it helps, Tsjerk 2011/8/17 Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw: Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. I think they should give the same result. If not, then the mostly likely explanation is that you've not used the files the way you think you have. You need to be able to issue grompp -f md -c pr -o md g_rms -s md.tpr -f whatever g_rms -s pr.gro -f whatever and get different results for there to be some kind of problem. In any case, you need to provide copies of your command lines and the different result in order for us to see whether you or GROMACS has done something wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do something else with our time :-) Mark Hi, I checked the result again The order of the different is less than 0.1 nm. So that means this different is caused by precision? Sincerely yours, Hsin-Lin -- 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] Velocity of atom
Nilesh Dhumal wrote: Hello, How can I print/calculate on velocity of a atom. g_traj -Justin I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] Regarding xtc
Dear Abraham, Thank you for your previous suggestion, I included nstxout, nsrvout and xtc_precision to output control. Now I am getting .xtc file but still it shows nothing in VMD but it read the frames while starting. Thank you. -- 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] Regarding xtc
Ravi Kumar Venkatraman wrote: Dear Abraham, Thank you for your previous suggestion, I included nstxout, nsrvout and xtc_precision to output control. Now I am getting .xtc file but still it shows nothing in VMD but it read the frames while starting. You need to load a coordinate file first, then load the .xtc as data for it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water
Hmm. Even now, I'm noticing problems with what I sent: It should be; rcoulomb = 1.3. For PME, rlist should equal rcoul. PME-switch can improve energy conservation, but the wrong PME-switch parameters can affect the results too much. PME w/o switch should be appropriate for most 'standard' usage. In the next month or so (by 4.6 at least), the manual will include some more guidance on accuracy in cutoffs. Summarizing again: For pretty good energy conservation, I would suggest: rlist = 1.3 coulombtype = PME rcoulomb = 1.3 vdw-type = Switch rvdw-switch = 1.0 rvdw = 1.1 This should work quite well -- you might get some drift after 1-2 ns, but not much. I'm working on developing suggested PME parameters right now for highly quantitative work, but it's not quite ready yet. Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- 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: Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, August 22, 2011. For all questions about CloudBroker and the CloudBroker Platform, please contact the company under i...@cloudbroker.com or Nicola Fantini under nicola.fant...@cloudbroker.com. If you need to talk to me in person for urgent or important issues, please call my mobile phone number. Kind regards, Wibke Sudholt -- Dr. Wibke Sudholt CEO CloudBroker GmbH Technoparkstrasse 1 CH-8005 Zurich Switzerland Phone: +41 44 633 79 34 Email: wibke.sudh...@cloudbroker.com Web:http://www.cloudbroker.com -- 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] Tutorial
I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Thank you -- 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] Force field for thiocyanate ions
Hi, Does anyone know about availability of MM pair-wise additive forcefield for thiocyanate anion ( SCN- ) , either in CHARMM or OPLS format ? Sanku-- 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] Tutorial
Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl http://inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Then Google again :) If you search Inflategro it is the first result that comes up. Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial: Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tutorial
Thank you yes i removed the Remove unnecessary lines ... i found the inflategro.pl when i click on the rl inflategro.pl it gives me Firefox can't find the server at inflategro.pl. http://inflategro.pl/ On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.** vt.edu/Pages/Personal/justin/**gmx-tutorials/membrane_** protein/02_topology.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl http://inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Then Google again :) If you search Inflategro it is the first result that comes up. Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial: Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tutorial
ok i did find the script thank you On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller sarabiocomputat...@gmail.com wrote: Thank you yes i removed the Remove unnecessary lines ... i found the inflategro.pl when i click on the rl inflategro.pl it gives me Firefox can't find the server at inflategro.pl. http://inflategro.pl/ On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul jalem...@vt.eduwrote: Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.* *vt.edu/Pages/Personal/justin/**gmx-tutorials/membrane_** protein/02_topology.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl http://inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Then Google again :) If you search Inflategro it is the first result that comes up. Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial: Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tutorial
The author of InflateGRO, Christian Kandt, is now at Univ. of Bonn. All his work is here: http://www.csb.bit.uni-bonn.de/inflategro.html On 2011-08-17 03:03:50PM -0500, Sara baretller wrote: Thank you yes i removed the Remove unnecessary lines ... i found the inflategro.pl http://inflategro.pl/ when i click on the rl inflategro.plhttp://inflategro.pl/ it gives me Firefox can't find the server at inflategro.plhttp://inflategro.pl. http://inflategro.pl/ On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu wrote: Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.plhttp://inflategro.pl http://inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Then Google again :) If you search Inflategro it is the first result that comes up. Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial: Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-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.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Tutorial
HI in the tutorial , it says that the script has the instructions to follow but when i opened the script i didn't find any instructions please what does 14 stands for and 5 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat thank you On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller sarabiocomputat...@gmail.com wrote: ok i did find the script thank you On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller sarabiocomputat...@gmail.com wrote: Thank you yes i removed the Remove unnecessary lines ... i found the inflategro.pl when i click on the rl inflategro.pl it gives me Firefox can't find the server at inflategro.pl. http://inflategro.pl/ On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul jalem...@vt.eduwrote: Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem. **vt.edu/Pages/Personal/justin/**gmx-tutorials/membrane_** protein/02_topology.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl http://inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Then Google again :) If you search Inflategro it is the first result that comes up. Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial: Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tutorial
Hi so i did Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. After i use the cat KALP_newbox.gro dppc128_whole.gro system.gro when i check the file system.gro it has the protein and the lipid coordinates, however when i load to vmd to veiw , the VMD does not show anything , does any body have an idea what s wrong Thank you On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller sarabiocomputat...@gmail.com wrote: ok i did find the script thank you On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller sarabiocomputat...@gmail.com wrote: Thank you yes i removed the Remove unnecessary lines ... i found the inflategro.pl when i click on the rl inflategro.pl it gives me Firefox can't find the server at inflategro.pl. http://inflategro.pl/ On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul jalem...@vt.eduwrote: Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/membrane_**protein/02_topology.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl http://inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Then Google again :) If you search Inflategro it is the first result that comes up. Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial: Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tutorial
Sara baretller wrote: HI in the tutorial , it says that the script has the instructions to follow but when i opened the script i didn't find any instructions please what does 14 stands for and 5 perl inflategro.pl http://inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat 14 is a cutoff radius for deleting lipids. 5 is the grid spacing for the area measurement, if memory serves. Both terms are in Angstrom. -Justin thank you On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller sarabiocomputat...@gmail.com mailto:sarabiocomputat...@gmail.com wrote: ok i did find the script thank you On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller sarabiocomputat...@gmail.com mailto:sarabiocomputat...@gmail.com wrote: Thank you yes i removed the Remove unnecessary lines ... i found the inflategro.pl http://inflategro.pl/ when i click on the rl inflategro.pl http://inflategro.pl/ it gives me Firefox can't find the server at inflategro.pl http://inflategro.pl. http://inflategro.pl/ On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/02_topology.html http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl http://inflategro.pl http://inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Then Google again :) If you search Inflategro it is the first result that comes up. Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial: Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- 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] Tutorial
Sara baretller wrote: Hi so i did Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. After i use the cat KALP_newbox.gro dppc128_whole.gro system.gro when i check the file system.gro it has the protein and the lipid coordinates, however when i load to vmd to veiw , the VMD does not show anything , does any body have an idea what s wrong Then the file format is still broken in some way. -Justin Thank you On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller sarabiocomputat...@gmail.com mailto:sarabiocomputat...@gmail.com wrote: ok i did find the script thank you On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller sarabiocomputat...@gmail.com mailto:sarabiocomputat...@gmail.com wrote: Thank you yes i removed the Remove unnecessary lines ... i found the inflategro.pl http://inflategro.pl/ when i click on the rl inflategro.pl http://inflategro.pl/ it gives me Firefox can't find the server at inflategro.pl http://inflategro.pl. http://inflategro.pl/ On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/02_topology.html http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl http://inflategro.pl http://inflategro.pl I googled It and did not find it. Can you please send me the script or tell me where I can find it Then Google again :) If you search Inflategro it is the first result that comes up. Also I used the cat KALP_newbox.gro dppc128_whole.gro system.gro so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial: Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
Hi Matthew, Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled by me (on my machine) or by the sys-admin on Linux cluster or blue-gene. The simulations using 4.5.4 crashed giving LINCS error, which is not the case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled with me (on my machine) or by the sys-admin on Linux cluster/blue-gene. cheers, Itamar On 18 August 2011 01:48, Matthew Zwier mczw...@gmail.com wrote: Could be a system blowing up, or perhaps a mis-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried productive runs. Now, no matter what I did, it crashed after few ps's of free MD or during the PR runs. Few of the things I had tried are: 1. Running the simulations on different systems (OSX, linux or blue-gene). 2. Using single or double precision versions. 3. An equilibration stage, 1ns long with a time-step of 1fs, during which the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. 4. Running part of the equilibration stage as NVT and then switched to NPT. 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom. Finally I had moved back to 4.0.7 which worked like charm. I wonder if someone else had encounter something like this. Attached please find the mdp files I used. All the best, 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- 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/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: Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, August 22, 2011. For all questions about CloudBroker and the CloudBroker Platform, please contact the company under i...@cloudbroker.com or Nicola Fantini under nicola.fant...@cloudbroker.com. If you need to talk to me in person for urgent or important issues, please call my mobile phone number. Kind regards, Wibke Sudholt -- Dr. Wibke Sudholt CEO CloudBroker GmbH Technoparkstrasse 1 CH-8005 Zurich Switzerland Phone: +41 44 633 79 34 Email: wibke.sudh...@cloudbroker.com Web:http://www.cloudbroker.com -- 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] GROMACS 4.5.4 keep crashing all the time.
You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages Do this for 4.0.7 and 4.5.4, for which I trust that you have been using exactly identical test systems. If not, then please try it again while conserving the system. Chris. -- original message -- Hi Matthew, Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled by me (on my machine) or by the sys-admin on Linux cluster or blue-gene. The simulations using 4.5.4 crashed giving LINCS error, which is not the case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled with me (on my machine) or by the sys-admin on Linux cluster/blue-gene. cheers, Itamar On 18 August 2011 01:48, Matthew Zwier mczwier at gmail.com wrote: Could be a system blowing up, or perhaps a mis-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass itamar.kass at monash.edu wrote: Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried productive runs. Now, no matter what I did, it crashed after few ps's of free MD or during the PR runs. Few of the things I had tried are: 1. Running the simulations on different systems (OSX, linux or blue-gene). 2. Using single or double precision versions. 3. An equilibration stage, 1ns long with a time-step of 1fs, during which the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. 4. Running part of the equilibration stage as NVT and then switched to NPT. 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom. Finally I had moved back to 4.0.7 which worked like charm. I wonder if someone else had encounter something like this. Attached please find the mdp files I used. All the best, Itamar. -- 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] GROMACS 4.5.4 keep crashing all the time.
chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages I'd also add that we need a detailed description of the system, including force field used and any other special considerations (distance restraints, modified parameters, etc). An .mdp file would also be useful for the run that crashes. -Justin Do this for 4.0.7 and 4.5.4, for which I trust that you have been using exactly identical test systems. If not, then please try it again while conserving the system. Chris. -- original message -- Hi Matthew, Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled by me (on my machine) or by the sys-admin on Linux cluster or blue-gene. The simulations using 4.5.4 crashed giving LINCS error, which is not the case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled with me (on my machine) or by the sys-admin on Linux cluster/blue-gene. cheers, Itamar On 18 August 2011 01:48, Matthew Zwier mczwier at gmail.com wrote: Could be a system blowing up, or perhaps a mis-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass itamar.kass at monash.edu wrote: Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried productive runs. Now, no matter what I did, it crashed after few ps's of free MD or during the PR runs. Few of the things I had tried are: 1. Running the simulations on different systems (OSX, linux or blue-gene). 2. Using single or double precision versions. 3. An equilibration stage, 1ns long with a time-step of 1fs, during which the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. 4. Running part of the equilibration stage as NVT and then switched to NPT. 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom. Finally I had moved back to 4.0.7 which worked like charm. I wonder if someone else had encounter something like this. Attached please find the mdp files I used. All the best, Itamar. -- 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] Force field for thiocyanate ions
On 18/08/2011 5:07 AM, Sanku M wrote: Hi, Does anyone know about availability of MM pair-wise additive forcefield for thiocyanate anion ( SCN- ) , either in CHARMM or OPLS format ? Sanku Google can suggest some possible leads. 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] GROMACS 4.5.4 keep crashing all the time.
Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro The em.mdp: integrator = steep maximum number of steps to integrate nsteps = 5 ;Energy minimizing stuff emstep = 0.001 emtol= 100.0 ; OPTIONS FOR BONDS constraints = none ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; Energy monitoring energygrps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist= 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-rf = 62 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Center of mass control nstcomm = 1000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode= linear ; Groups for center of mass motion removal comm-grps= system the pr.mdp: define = -DPOSRES integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100ps. ; OPTIONS FOR BONDS ; Constrain control constraints = all-bonds ; Do not constrain the start configuration continuation = no ; Type of constraint algorithm constraint-algorithm = lincs ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout = 10 nstfout = 10 ; Output frequency and precision for xtc file nstxtcout= 5000 xtc-precision= 1000 ; Energy monitoring energygrps = Protein Non-protein nstenergy= 5000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist= 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62; As suggested at J Comput Chem. 2004 Oct;25(13):1656-76. vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 290K - do not get velocity from gro file. gen_vel = yes gen_temp= 290 gen-seed= -1 ; Center of mass control nstcomm = 1000 ;
Re: [gmx-users] converting cpt between single and double precision
On 18/08/2011 3:07 AM, Peter C. Lai wrote:
On 2011-08-16 08:16:52PM -0500, Mark Abraham wrote:
On 17/08/2011 6:13 AM, Peter C. Lai wrote:
Is there a way to convert between single and double precision cpt files so
I can use double precision grompp on it to change some parameters but still
keep state information for continuity?
Or can I just trjconv_d the last frame of the single precision trr and feed
that to grompp -t?
(A machine I am using for preprocessing only has double precision tools and
it would be difficult to have both versions installed.)
Any GROMACS tool can read any of its binary formats written in either
precision, and write only in the precision with which the tool was compiled.
The problem is that when I use a double precision grompp and -t a single
precision .cpt, I get notices that it is discarding state data due to the
precision mismatch.
This is on 4.5.4:
Will read whole trajectory
Velocities generated: ignoring velocities in input trajectory
Precision mismatch for state entry box, code precision is double, file
precision is float
Precision mismatch for state entry box-rel, code precision is double, file
precision is float
Precision mismatch for state entry box-v, code precision is double, file
precision is float
Precision mismatch for state entry pres_prev, code precision is double, file
precision is float
Precision mismatch for state entry x, code precision is double, file precision
is float
Precision mismatch for state entry v, code precision is double, file precision
is float
the gmxdump of the resuling tpr confirms this:
boxv (3x3):
boxv[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev (3x3):
pres_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev (3x3):
svir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev (3x3):
fvir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
nosehoover_xi: not available
Interestingly enough, box and box_rel are preserved, despite the messages
to the contrary, but of course, the majority of the reason to use .cpt
is to transfer the velocities and virial...
OK, that seems inconsistent. I would suppose there should be some
capacity to interconvert precision by truncation/extension of the
precision of these values - perhaps with a command line option to force
that. Please file an issue at redmine.gromacs.org attaching input files
and how to reproduce the issue.
Mark
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Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
On 18/08/2011 10:14 AM, Itamar Kass wrote: Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro So you're doing solvated EM, then position-restrained NPT MD, then NPT. Sounds to me like you might have a bad initial contact that can't relax under solvated EM, nor under PR-NPT, and is getting numerically lucky in 4.0.7 and not under 4.5.4. If so, then careful inspection of the start of the 4.0.7 run might show this. Vacuo EM of the solute might help if the problem is intra-solute. Have you explored the suggestions here? http://www.gromacs.org/Documentation/Terminology/Blowing_Up 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] GROMACS 4.5.4 keep crashing all the time.
I concur with what Mark suggested about in vacuo EM. I would also point out the following problem(s): and the md.mdp: Here you call for 300 K as the reference temperature and the temperature at which you've equilibrated: tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 290K - do not get velocity from gro file. And here you're destroying the previous equilibration by re-generating velocities and simultaneously generating velocities for the wrong temperature, which may or may not induce instability into the system. gen_vel = yes gen_temp= 290 gen-seed= -1 -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
Dear Mark, We also tried to minimise the system in vacuum before adding water and ions withou, but it still crashed when we did MD. Itamar. On 18/08/2011, at 10:31 AM, Mark Abraham wrote: On 18/08/2011 10:14 AM, Itamar Kass wrote: Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro So you're doing solvated EM, then position-restrained NPT MD, then NPT. Sounds to me like you might have a bad initial contact that can't relax under solvated EM, nor under PR-NPT, and is getting numerically lucky in 4.0.7 and not under 4.5.4. If so, then careful inspection of the start of the 4.0.7 run might show this. Vacuo EM of the solute might help if the problem is intra-solute. Have you explored the suggestions here? http://www.gromacs.org/Documentation/Terminology/Blowing_Up 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 - 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/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] Segmentation fault after mdrun for MD simulation
Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.048739, max 1.100685 (between atoms 8422 and 8421) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length .. .. snip .. .. starting mdrun 'TUBULIN ALPHA CHAIN' 25000 steps, 50.0 ps. Warning: 1-4 interaction between 8443 and 8446 at distance 2.853 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 .. .. snip .. .. step 0: Water molecule starting at atom 23781 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1# Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1# Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2# Back Off! I just backed up step0b_n3.pdb to ./#step0b_n3.pdb.2# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1# Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2# Back Off! I just backed up step0c_n3.pdb to ./#step0c_n3.pdb.2# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates ^Mstep 0/opt/sge/jacobson/spool/node-2-05/job_scripts/1097116: line 21: 1473 Segmentation fault (core dumped) $MDRUN -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s 1JFF_md.tpr -o 1JFF_md.trr -c 1JFF_pmd.gro -x 1JFF_md.xtc -e 1JFF_md.edr On 16 August 2011 10:58, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Hi, I get the error Atomtype CR1 not found when I execute grompp. After perusing the gmx archives, I understand this error has to do with the lack of CR1 being specified in the force field. However, I did include the appropriate .itp files in my .top file (shown below). As you can see, obviously CR1 is specified in taxol.itp and gtp.itp. Therefore, I'm not sure what exactly is the problem here. You're mixing and matching force fields.
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
Hi Justing, I had reinitialised the systems after the PR run but I don't think this is the origin of the error. Because the system with the Ca crashed allways in the PR state, although the systems run with 4.0.7 done it fine. Best, Itamnar On 18/08/2011, at 10:39 AM, Justin A. Lemkul wrote: I concur with what Mark suggested about in vacuo EM. I would also point out the following problem(s): and the md.mdp: Here you call for 300 K as the reference temperature and the temperature at which you've equilibrated: tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 290K - do not get velocity from gro file. And here you're destroying the previous equilibration by re-generating velocities and simultaneously generating velocities for the wrong temperature, which may or may not induce instability into the system. gen_vel = yes gen_temp= 290 gen-seed= -1 -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists - 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/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] Segmentation fault after mdrun for MD simulation
rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length If mdrun is failing at step 0, it indicates that your system is physically unreasonable. Either the starting configuration has atomic clashes that have not been resolved (and thus you need better EM and/or equilibration) or that the parameters assigned to the molecules in your system are unreasonable. -Justin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.048739, max 1.100685 (between atoms 8422 and 8421) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length .. .. snip .. .. starting mdrun 'TUBULIN ALPHA CHAIN' 25000 steps, 50.0 ps. Warning: 1-4 interaction between 8443 and 8446 at distance 2.853 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 .. .. snip .. .. step 0: Water molecule starting at atom 23781 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1# Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1# Back Off! I just backed up step0b_n5.pdb to ./#step0b_n5.pdb.2# Back Off! I just backed up step0b_n3.pdb to ./#step0b_n3.pdb.2# Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1# Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1# Back Off! I just backed up step0c_n5.pdb to ./#step0c_n5.pdb.2# Back Off! I just backed up step0c_n3.pdb to ./#step0c_n3.pdb.2# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates ^Mstep 0/opt/sge/jacobson/spool/node-2-05/job_scripts/1097116: line 21: 1473 Segmentation fault (core dumped) $MDRUN -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s 1JFF_md.tpr -o 1JFF_md.trr -c 1JFF_pmd.gro -x 1JFF_md.xtc -e 1JFF_md.edr On 16 August 2011 10:58, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Hi, I get the error Atomtype CR1 not found when I execute grompp. After perusing the gmx archives, I
[gmx-users] GROMACS 4.5.4 keep crashing all the time
run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.neale at utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro The em.mdp: integrator = steep maximum number of steps to integrate nsteps = 5 ;Energy minimizing stuff emstep = 0.001 emtol= 100.0 ; OPTIONS FOR BONDS constraints = none ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; Energy monitoring energygrps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist= 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-rf = 62 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Center of mass control nstcomm = 1000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode= linear ; Groups for center of mass motion removal comm-grps= system the pr.mdp: define = -DPOSRES integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100ps. ; OPTIONS FOR BONDS ; Constrain control constraints = all-bonds ; Do not constrain the start configuration continuation = no ; Type of constraint algorithm constraint-algorithm = lincs ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout = 10 nstfout = 10 ; Output frequency and precision for xtc file nstxtcout= 5000 xtc-precision= 1000 ; Energy monitoring energygrps = Protein Non-protein nstenergy= 5000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist= 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62; As suggested at J Comput Chem. 2004 Oct;25(13):1656-76. vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 290K
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.ne...@utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.neale at utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro The em.mdp: integrator = steep maximum number of steps to integrate nsteps = 5 ;Energy minimizing stuff emstep = 0.001 emtol= 100.0 ; OPTIONS FOR BONDS constraints = none ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; Energy monitoring energygrps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist= 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-rf = 62 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Center of mass control nstcomm = 1000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode= linear ; Groups for center of mass motion removal comm-grps= system the pr.mdp: define = -DPOSRES integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100ps. ; OPTIONS FOR BONDS ; Constrain control constraints= all-bonds ; Do not constrain the start configuration continuation = no ; Type of constraint algorithm constraint-algorithm = lincs ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout= 10 nstfout= 10 ; Output frequency and precision for xtc file nstxtcout = 5000 xtc-precision = 1000 ; Energy monitoring energygrps = Protein Non-protein nstenergy = 5000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist= 5 ; ns algorithm (simple or grid) ns-type= Grid ; nblist cut-off rlist = 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62; As suggested at J Comput Chem. 2004 Oct;25(13):1656-76. vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure
[gmx-users] GROMACS 4.5.4 keep crashing all the time
OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the same lincs warnings? 6. Also, note that you are getting warnings and the run does not actually crash but just stops after too many warnings. So what are atoms 981 and 982? Does their motion look different in an important ways between the 4.0.7 and 4.5.4 trajectories? Chris. -- original message -- Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: -- 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] Not receiving replies
Respected Sir, I am not receiving reply mails to my gmail id, even when it is answered. Kindly check Sir. Thank you With Regards M. Kavyashree -- 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] Not receiving replies
Kavyashree M wrote: Respected Sir, I am not receiving reply mails to my gmail id, even when it is answered. Kindly check Sir. You can check your subscription options here (under gmx-users Subscribers enter your email address and click Unsubscribe or edit options): http://lists.gromacs.org/mailman/listinfo/gmx-users You can see what type of subscription you have (individual or digest), etc. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
Dear all: I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system. I have a question. When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions: 1. I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible? 2. I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? Thanks for any reply. Best wishes, KONG Xian Tsinghua, Beijing, China -- 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] mdrun did not support large file offsets
Dear gmx-users, When I continued a run on my x86_64 linux clusters using the command mdrun -deffnm prod -cpi prod.cpt -append, I got the errors as below: Program mdrun, VERSION 4.5.4 Source code file: checkpoint.c, line: 1734 Fatal error: The original run wrote a file called 'prod.xtc' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I also tried to recompile gromacs with alternative option --enable-largefile, but it still could not work. Then I compared the config.log generated using --enable-largefile and --disable-largefile (default) after configured, however, the two files were almost the same. How to solve this problem? Any suggestions are appreciated. Thanks in advance. Best regards, Bo -- 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] Segmentation fault after mdrun for MD simulation
Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line: $mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md.log to ./#md.log.2# Reading file 1JFF_em.tpr, VERSION 4.5.3 (single precision) Starting 24 threads Will use 15 particle-particle and 9 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 2.92429 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I figure the problem must lie within my em.mdp file: title = 1JFF cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 1 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 ~ I figure this is an issue related to with PME and the Fourier spacing? Thanks, rainy908 On 17 August 2011 17:55, Justin A. Lemkul jalem...@vt.edu wrote: rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length If mdrun is failing at step 0, it indicates that your system is physically unreasonable. Either the starting
Re: [gmx-users] Segmentation fault after mdrun for MD simulation
On 18/08/2011 2:41 PM, rainy908 wrote: Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line: $mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md.log to ./#md.log.2# Reading file 1JFF_em.tpr, VERSION 4.5.3 (single precision) Starting 24 threads Will use 15 particle-particle and 9 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 2.92429 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I figure the problem must lie within my em.mdp file: It could, but if you follow the above advice you will learn about some other considerations. Mark title = 1JFF cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.001 ; ps ! nsteps = 1 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 ~ I figure this is an issue related to with PME and the Fourier spacing? Thanks, rainy908 On 17 August 2011 17:55, Justin A. Lemkuljalem...@vt.edu wrote: rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by the awkward positioning of atoms 8443 and 8446 with respect to one another, but am not 100%. Any advice would be especially welcome. My files are as follows: md.mdp title = 1JFF MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.0001 ; ps nsteps = 25000 ; nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl= berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529 error output file: .. .. Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file 1JFF_md.tpr, VERSION 4.5.3 (single precision) Starting 8 threads Loaded with Money Making 3D domain decomposition 2 x 2 x 2 Back Off! I just backed up 1JFF_md.trr to ./#1JFF_md.trr.1# Back Off! I just backed up 1JFF_md.edr to ./#1JFF_md.edr.1# Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.046849, max 1.014038 (between atoms 8541 and 8539) Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001453, max 0.034820 (between atoms 315 and 317) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30
