Dear all,<br><br>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.<br><br>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.<br>
<br>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: <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 check the <b>state.cpt</b> file using <b>gmxdump</b> 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: <b>box-v (3x3)</b> and <b>thermostat-integral</b>.<br>
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?<br><br>Your suggestions are greatly helpful and appreciated.<br>
<br>Justin Zhang<br> <br><br><br><div class="gmail_quote">在 2010年6月25日 下午4:45，张春雷 <span dir="ltr"><<a href="mailto:chunleizhang.pku@gmail.com">chunleizhang.pku@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;">
Information shown by gmxcheck:<br><br><b>Checking file state.cpt</b><br><br># Atoms 9817<br>Last frame -1 time 360000.000 <br><br><br>Item #frames Timestep (ps)<br>Step 1<br>Time 1<br>
Lambda 1<br>Coords 1<br>Velocities 1<br>Forces 0<br>Box 1<br><br><b>Checking file state_prev.cpt</b><br><br># Atoms 9817<br>Last frame -1 time 359010.000 <br><br>
<br>Item #frames Timestep (ps)<br>Step 1<br>Time 1<br>Lambda 1<br>Coords 1<br>Velocities 1<br>Forces 0<br>Box 1<br><br><b>Checking file md_360ns.trr</b><br>
trn version: GMX_trn_file (double precision)<br>Reading frame 0 time 0.000 <br># Atoms 9817<br>Reading frame 2000 time 300000.000 <br><br><br>Item #frames Timestep (ps)<br>Step 2401 150<br>
Time 2401 150<br>Lambda 2401 150<br>Coords 2401 150<br>Velocities 2401 150<br>Forces 0<br>Box 2401 150<br><br>Is anything wrong? <br><br><br><div class="gmail_quote">
2010/6/25 Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>></span><div><div></div><div class="h5"><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><br><br>----- Original Message -----<br>From: 张春雷 <<a href="mailto:chunleizhang.pku@gmail.com" target="_blank">chunleizhang.pku@gmail.com</a>><br>Date: Friday, June 25, 2010 16:46<br>Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have tried another approach in which the checkpoint file is neglected.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>$mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g md_720ns.log<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation.<br>
<br></div>What does gmxcheck say about all the files involved?<br><font color="#888888"><br>Mark</font><div><div></div><div><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Have you encountered similar things?<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Thank you for your suggestions!<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><div class="gmail_quote"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>在 2010年6月25日 上午9:16，weixin <span dir="ltr"><<a>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><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </div>
<div><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>How about using the last .gro file to continue your simulation?</div> <div><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </div>
<div class="gmail_quote"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>2010/6/24 张春雷 <span dir="ltr"><<a>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><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Dear GMX-users,<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>This is Justin. <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> I have successfully completed a 360ns simulation, during which the time step is 30 fs.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I would like to extend the simulation to 1micro-second. The commands I used are:<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>$tpbconv_mpi_d -s md_360ns.tpr -extend 360000 -o md_720ns.tpr<br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>$mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>However, I received the following message:<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Checkpoint file is from part 1, new output files will be suffixed part0002.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Getting Loaded...<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Loaded with Money<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>starting mdrun 'Protein in POPE bilayer'<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> 24000000 steps, 720000.0 ps (continuing from step 12000000, 360000.0 ps).<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>step 12000000, remaining runtime: 0 s <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>p0_6991: p4_error: interrupt SIGSEGV: 11<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have searched the mail-list, but found no similar report. I also search through google, but no answer seems satisfactory.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I once performed extending simulation for all atom simulation, and the method mentioned above worked.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Is anyone familiar with MARTINI CG simulation?<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Could you give me some suggestions?<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Many thanks!<br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Justin<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
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