Hi,<br><br>How big is your file? I assume since you are running 180000ps simulation, it might be big. I remember there's a problem with gromacs not being able to truncate file size >4Gb. <br><br>Greg<br><br><div class="gmail_quote">
On Tue, Sep 7, 2010 at 8:04 AM, David de Sancho <span dir="ltr"><<a href="mailto:daviddesancho@gmail.com">daviddesancho@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Gromacs users<br>I am experiencing a problem with restarts in a REMD simulation with explicit solvent in Gromacs 4.0.5. I am trying to continue a set of simulations that finished after the maximum time in our cluster queue had been reached. Therefore I just directly (i.e. without modifying my input file with tpbconv) try continuing my run using <br>
<br>mpiexec "bindir"/mdrun_openmpi_intel -multi 32 -replex 5000 -v -s tprfile.tpr -x xtcfile.xtc -o trrfile.trr -c grofile.gro -e enefile.ene -g logfile.log -cpi cptfile.cpt -cpo cptfile.cpt -append<br><br>This has worked before in previous continuations of this REMD simulation, so in principle the pbs script I am using should be fine. However, now I find two types of error messages: <br>
<br>(1) Reading checkpoint file cptfile{i}.cpt generated: ***<br>#PME-nodes mismatch,<br>current program: -1<br> checkpoint file: 0<br>Gromacs binary or parallel settings not identical to previous run.<br>Continuation is exact, but is not guaranteed to be binary identical.<br>
<br>(2) Fatal error:<br>Truncation of file xtcfile${i}.xtc failed.<br><br>I have been browsing the lists and apparently the first problem is not very important. However the second error, reached after loading the tpr and cpt files, is fatal. I have thus checked what the problem was with my xtc files by running gmxcheck on them and obtained messages like<br>
<br># Atoms 6950<br>Precision 0.001 (nm)<br>Reading frame 90000 time 180000.016 <br><br>Item #frames Timestep (ps)<br>Step 90878 2<br>Time 90878 2<br>Lambda 0<br>Coords 90878 2<br>
Velocities 0<br>Forces 0<br>Box 90878 2<br><br>Nothing here tells me much about what can be going wrong. Also, I have looked at the last frame of the simulation using vmd in case there were missing atoms in my protein but it definitely looks like there is nothing wrong. I have tried with the cpt and prev.cpt files in case there was something wrong with the cpt file but still I got the fatal error.<br>
Any hints on what it is that I am doing wrong?<br>Thanks<br><font color="#888888"><br><br>David<br><br><br><br>
</font><br>--<br>
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