[gmx-developers] From .tpr to .gro+.top+.mdp

Nayden Markatchev markatchev at gmail.com
Mon Oct 23 08:19:43 CEST 2006

Thanks Mark.  Your description is very helpful.  Much appreciated.


On 10/22/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Nayden Markatchev wrote:
> > Hello,
> >
> > My group started experimenting with the idea of mutable and migratable
> > jobs across clusters and gromacs is the first application we tried.
> > Moving the job is made easy because of the portable format of the .tpr
> > file, but we run into a problem when we want to reconfigure a job.  I
> > did a bit of searching around, but I couldn't find information on how
> > to do that, so I resorted in posting in the gromacs-users mailing
> > list.  My question was, provided I have a .tpr file, and I lack .gro,
> > .top, and .mdp files, is is possible to reconfigure that file to be
> > run on a different number of nodes that it was originally configured
> > for.  I was told that the this is not possible but I wonder why this
> > is the case.  Because of the nature of my second question, I thought
> > that this mailing list is the more appropriate place for it.
> The reason will include the decomposition of the grid search algorithm
> to multiple processors (see section 3.4.2 in manual) and presumably more
> (and uglier!) such stuff if PME is being used.
> Regenerating an equivalent .mdp file is fairly straightforward, since
> the input record is in the .tpr file (see gmxdump output). You don't
> want to regenerate just a .gro file because you will lose precision. You
> want to regenerate a .trr and .edr file for the data, and a .gro file
> just for atom names. This is fiddly but doable. Regenerating an
> equivalent .top file would be possible, but far too much work to be
> worth doing for the gain cases of 1) rescuing a user who deleted their
> own topology and 2) trying to do a transparent migration of cpu size.
> If you want mutability, write a wrapper job submission script that takes
> the original {trr,edr,gro,top,mdp} grompp input set as its input and
> decides at runtime how many cpus to use and generate the .tpr file then.
> Mark
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