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 <[email protected]>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 <[email protected]> > > >> >> ----- Original Message ----- >> From: 张春雷 <[email protected]> >> 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 <[email protected]> >> >> > 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 <[email protected]>写道： >> >>> > >>> > How about using the last .gro file to continue your simulation? >>> > >>> > >>> > >>> > 2010/6/24 张春雷 <[email protected]> >>> >>>> > 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 [email protected] >>>> > 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/search before >>>> posting! >>>> > Please don't post (un)subscribe requests to the list. Use the >>>> > www interface or send it to [email protected]. >>>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> > >>> > >>> > -- >>> > gmx-users mailing list [email protected] >>> > 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/search before >>> posting! >>> > Please don't post (un)subscribe requests to the list. Use the >>> > www interface or send it to [email protected]. >>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> > >> > -- >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
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