[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel

Xavier Periole X.Periole at rug.nl
Thu Oct 18 15:59:39 CEST 2007

> This question is about trying to make sure that I am doing the right thing
> while trying to use tpbconv to restart jobs.
> After minimization, for the first dynamics run, I use gen_vel = yes. For
> subsequent restart runs however, gen_vel must be set to no. After the first
> dynamics run of 200ps, my output is mol-1.edr/trr, and the input for the
> first dynamics run was mol-1.tpr
> I can then try to extend the simulation beyond 200 ps using tpbconv with the
> following options:
> tpbconv -f mol-1.trr -s mol-1.tpr -e mol-1.edr -extend 200 -o mol-2.tpr

This is correct. tpbconv will take the velocities in the mol-1.tpr

> The problem with this, however, is that mol-1.tpr was built with gen_vel =
> yes, which should not be the case when one is restarting the simulation.
>First question: will this matter at all, because the velocities should be
> read from the .trr file anyway, and that should overwrite the information in
> the tpr file ?
> In order to circumvent the problem, and avoid deshuffling and reshuffling, I
> wrote another .tpr file for the first dynamics run but with gen_vel set to
> no. I did not use this tpr file to run the simulation. Lets call this tpr
> file mol-novelocity-1.tpr. So, the only difference between mol-1.tpr and
> mol-novelocity-1.tpr is that the former has initialized velocities, while
> the latter does not.

Good trial but this will not work! It is not possible to have a tpr file
without velocities. If you set gen_v to no and do not give a gro/tpr/trr
file for it to read the velocities it will generate new ones anyways.

> Now, I can use tpbconv to restart the simulation as follows:
> tpbconv -s mol-1.tpr -f mol-1.trr  -e mol-1.edr -extend 200 -o mol-2.tpr
> I just wanted to confirm if what I am doing makes sense ? Thanks very much
> for the help !
> -Himanshu

XAvier Periole - PhD

- Institute of Molecular Assemblies
      City University of New York - USA
- Molecular Dynamics-Group
      University of Groningen - The Netherlands

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