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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 18 15:53:20 CEST 2007

himanshu khandelia wrote:
> Hi
> This question is about trying to make sure that I am doing the right 
> thing while trying to use tpbconv to restart jobs.

Check out http://wiki.gromacs.org/index.php/Doing_Restarts

> 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
> 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 ?

gen_vel is only used by grompp

> 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.
> 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 !

These two output .tpr files should be the same except for the initial 
steps and times, unless your mol-2.mdp file took care of that. You can 
use gmxcheck to test for the differences.

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