Hi Justin, what kind of error message do you get if you run this system on a single core without MPI?
Carsten On Jul 8, 2010, at 9:36 PM, 张春雷 wrote: > Dear all, > > I have post this question about a two weeks ago. During these days, I > followed suggestions from Mark and weixin, but did not fix it. Here, I repeat > it again to seek more help. > > I attempt to extend MD simulation for a coarse-grained system. CG models are > in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. > > I tried to use check point file state.cpt to extend my simulation. The mdrun > program can read to the check file. But it reported error like this: > > Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 > > Loaded with Money > > starting mdrun 'Protein in POPE bilayer' > 24000000 steps, 720000.0 ps (continuing from step 12000000, 360000.0 ps). > step 12000000, remaining runtime: 0 s > p0_6991: p4_error: interrupt SIGSEGV: 11 > > I check the state.cpt file using gmxdump and compare it with other checkpoint > files that can be used for extending All-atom simulations. I found that in > the CG check point file, some sections are missing: box-v (3x3) and > thermostat-integral. > I am not sure whether this missing sections cause my run crash. If it is, > could any one tell me possible reasons that result in the loss of box-v and > thermostat-integral and how to fix the problem? > > Your suggestions are greatly helpful and appreciated. > > Justin Zhang > > > > 在 2010年6月25日 下午4:45,张春雷 <chunleizhang....@gmail.com>写道: > Information shown by gmxcheck: > > Checking file state.cpt > > # Atoms 9817 > Last frame -1 time 360000.000 > > > Item #frames Timestep (ps) > Step 1 > Time 1 > Lambda 1 > Coords 1 > Velocities 1 > Forces 0 > Box 1 > > Checking file state_prev.cpt > > # Atoms 9817 > Last frame -1 time 359010.000 > > > Item #frames Timestep (ps) > Step 1 > Time 1 > Lambda 1 > Coords 1 > Velocities 1 > Forces 0 > Box 1 > > Checking file md_360ns.trr > trn version: GMX_trn_file (double precision) > Reading frame 0 time 0.000 > # Atoms 9817 > Reading frame 2000 time 300000.000 > > > Item #frames Timestep (ps) > Step 2401 150 > Time 2401 150 > Lambda 2401 150 > Coords 2401 150 > Velocities 2401 150 > Forces 0 > Box 2401 150 > > Is anything wrong? > > > 2010/6/25 Mark Abraham <mark.abra...@anu.edu.au> > > > > ----- Original Message ----- > From: 张春雷 <chunleizhang....@gmail.com> > Date: Friday, June 25, 2010 16:46 > Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > The last .gro file only provides coordinates of the system. No velocity is > > recorded. Actually, what I attempt to achieve is a binary identical > > trajectory. So I think the velocity from the last step is critical. > > > > I have tried another approach in which the checkpoint file is neglected. > > > > $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g > > md_720ns.log > > > > It works. So the checkpoint file appears to contain some error. But it is > > generated by a normally finished production simulation. > > What does gmxcheck say about all the files involved? > > Mark > > > > Have you encountered similar things? > > > > Thank you for your suggestions! > > > > > > > > 在 2010年6月25日 上午9:16,weixin <xwx...@gmail.com>写道: > > > > How about using the last .gro file to continue your simulation? > > > > > > > > 2010/6/24 张春雷 <chunleizhang....@gmail.com> > > Dear GMX-users, > > > > This is Justin. > > I am performing coarse-grained simulation on a protein-lipid bilayer > > system. This is a MARTINI CG model. > > I have successfully completed a 360ns simulation, during which the time > > step is 30 fs. > > > > I would like to extend the simulation to 1micro-second. The commands I used > > are: > > > > $tpbconv_mpi_d -s md_360ns.tpr -extend 360000 -o md_720ns.tpr > > > > $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g > > md_360ns.log -cpi state.cpt > > > > However, I received the following message: > > > > Checkpoint file is from part 1, new output files will be suffixed part0002. > > Getting Loaded... > > Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) > > > > Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 > > > > Loaded with Money > > > > starting mdrun 'Protein in POPE bilayer' > > 24000000 steps, 720000.0 ps (continuing from step 12000000, 360000.0 ps). > > step 12000000, remaining runtime: 0 s > > p0_6991: p4_error: interrupt SIGSEGV: 11 > > > > I have searched the mail-list, but found no similar report. I also search > > through google, but no answer seems satisfactory. > > > > I once performed extending simulation for all atom simulation, and the > > method mentioned above worked. > > > > Is anyone familiar with MARTINI CG simulation? > > Could you give me some suggestions? > > > > Many thanks! > > > > Justin > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search > > before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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