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. 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 >> 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
