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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