----- 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 > 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
-- 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
