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

himanshu khandelia hkhandelia at gmail.com
Thu Oct 18 15:48:06 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

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.

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 !

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071018/d6be960f/attachment.html>

More information about the gromacs.org_gmx-users mailing list