[gmx-users] Extending an mdrun with trr >2GB

David spoel at xray.bmc.uu.se
Sat Mar 27 11:11:01 CET 2004

On Sat, 2004-03-27 at 10:57, Martina Bertsch, PhD wrote:
> Hi, David.
> I am not sure what you mean. On our cluster, my home directory with
> gmx data and the trr > 2.2 GB is already NFS mounted on all nodes.
> What would I do next?

You probably need to mount the disk using NFS v 3. Did you try it
directly on the disk server?
> As I mentioned earlier, the command:
> tpbconv -s full.tpr -f full.trr -o full_extend_1.tpr -extend 10000
> does not work, because the full.trr "cannot be found". Peter Zoon
> suggested compressing trr into xtc format, but that will not work,
> because you need velocity information to continue or extend a run. 
> Would it be terribly wrong if I simply started a new 10-ns simulation
> with the final coordinates from the first trr:
It wouldn't be the same.

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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