Dear Gromacs users 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
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 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: (1) Reading checkpoint file cptfile{i}.cpt generated: *** #PME-nodes mismatch, current program: -1 checkpoint file: 0 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. (2) Fatal error: Truncation of file xtcfile${i}.xtc failed. 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 # Atoms 6950 Precision 0.001 (nm) Reading frame 90000 time 180000.016 Item #frames Timestep (ps) Step 90878 2 Time 90878 2 Lambda 0 Coords 90878 2 Velocities 0 Forces 0 Box 90878 2 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. Any hints on what it is that I am doing wrong? Thanks David
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