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.<br><br>I have tried another approach in which the checkpoint file is neglected.<br>
<br>$mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g
md_720ns.log<br><br>It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation.<br>Have you encountered similar things?<br><br>Thank you for your suggestions!<br>
<br><br><br><div class="gmail_quote">在 2010年6月25日 上午9:16，weixin <span dir="ltr"><<a href="mailto:xwxnju@gmail.com">xwxnju@gmail.com</a>></span>写道：<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div> </div>
<div>How about using the last .gro file to continue your simulation?</div>
<div><br><br> </div>
<div class="gmail_quote">2010/6/24 张春雷 <span dir="ltr"><<a href="mailto:chunleizhang.pku@gmail.com" target="_blank">chunleizhang.pku@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="padding-left: 1ex; margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204, 204, 204);"><div><div></div><div class="h5">Dear GMX-users,<br><br>This is Justin. <br>I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model.<br>
I have successfully completed a 360ns simulation, during which the time step is 30 fs.<br><br>I would like to extend the simulation to 1micro-second. The commands I used are:<br><br>$tpbconv_mpi_d -s md_360ns.tpr -extend 360000 -o md_720ns.tpr<br>
<br>$mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt<br><br>However, I received the following message:<br><br>Checkpoint file is from part 1, new output files will be suffixed part0002.<br>
Getting Loaded...<br>Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)<br><br>Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010<br><br>Loaded with Money<br><br>starting mdrun 'Protein in POPE bilayer'<br>
24000000 steps, 720000.0 ps (continuing from step 12000000, 360000.0 ps).<br>step 12000000, remaining runtime: 0 s <br>p0_6991: p4_error: interrupt SIGSEGV: 11<br><br>I have searched the mail-list, but found no similar report. I also search through google, but no answer seems satisfactory.<br>
<br>I once performed extending simulation for all atom simulation, and the method mentioned above worked.<br><br>Is anyone familiar with MARTINI CG simulation?<br>Could you give me some suggestions?<br><br>Many thanks!<br>
<br>Justin<br><br></div></div>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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