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

himanshu khandelia hkhandelia at gmail.com
Thu Oct 18 16:55:17 CEST 2007

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

Thanks very much.  I do understand the general restarting mechanism. It is
only the first restart that was a little bit confusing

> > 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.

Sorry I did not understand ? There is no mol-2.mdp file. So, in effect the
first tpbconf command should work. The velocities will be obtained from the
.trr file and not the .tpr file, correct ? That is the main issue bothering
me, because the .tpr file contains the initial velocities generated during
the first run.

tpbconv -f mol-1.trr -s mol-1.tpr -e mol-1.edr -extend 200 -o mol-2.tpr

Thanks again,

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