Hi,
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.
Greg
On Tue, Sep 7, 2010 at 8:04 AM, David de Sancho <daviddesan...@gmail.com>wrote:
> 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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