[gmx-users] Extending an mdrun with trr >2GB
spoel at xray.bmc.uu.se
Sat Mar 27 10:20:01 CET 2004
On Sat, 2004-03-27 at 10:10, Martina Bertsch, PhD wrote:
> If I understand correctly, trjconv converts the trr file to xtc format,
> which does *not* contain velocities or forces and thus saves space.
> Manuals specifically instruct us not to remove the trr file if a run has
> to be restarted.
You need the trr file. This is a linux problem that has been discussed
many times on the list. Apparently we need a FAQ entry. A possible
solution is to NFS mount the disk your trajectory is on and do it over
NFS. With a decently modern Linux it should not be a problem (we run
Redhat 8 and higher):
[rembrandt:octanol/XTC] % ls -l simE2.xtc
-rw-r--r-- 1 spoel xray 16029520596 Nov 15 21:15 simE2.xtc
> I don't think I would get a true continuation run without velocities. Am
> I correct?
> Peter Zoon wrote:
> > Hi!
> > with trjconv you can make full.trr smaller and thus overcome the
> > problem of file> 2GB
> > Then you can use this newly made file to restart, with tpbconv.
> > Cheers
> > Peter
> > At 09:18 3/27/2004, you wrote:
> >> Greetings.
> >> Our administrator had to install upgrades on the cluster, so I had to
> >> stop my mdrun of a protein in a POPC bilayer, which was running
> >> smoothly up until now (for 10 ns). To stop the run, I used the kill
> >> -USR1 signal. The signal produced a gro file, named
> >> "MT1_popc_postfull.gro", and the megaflops accounting report at the
> >> end of the log file, as if it were the end of the run. However, the
> >> run would have been continued for another 10 ns, if there had not
> >> been any interruption.
> >> When the upgrades were completed, I attempted to restart the run with
> >> the following command:
> >> tpbconv -s full.tpr -f full.trr -o full_extend_1.tpr -extend 10000
> >> I also tried the following:
> >> grompp -f full.mdp -t full.trr -c MT1_popc_postfull.gro -n index.ndx
> >> -p MT1_popc.top -o full_extend.tpr
> >> But in both cases, I received an error message:
> >> File full.trr not found.
> >> Of course, the file is actually present and larger than 2.2 GB.
> >> How do I continue/extend my mdrun? I could start a new 10 ns
> >> simulation with the final coordinates from MT1_popc_postfull.gro, but
> >> it would not be a true continuation run without the velocities from
> >> the first part of the run, since I could not read the trr file.
> >> Also, will I be able to analyze the trr trajectory that is larger
> >> than 2 GB with g_rms, g_hbond etc, or will I have to convert it to
> >> the xtc format?
> >> Thank you.
> >> Martina
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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