[gmx-users] query related to rerunning MD

Xavier Periole X.Periole at rug.nl
Mon Jan 28 10:40:25 CET 2008

On Mon, 28 Jan 2008 08:57:47 +0000 (GMT)
  Ragothaman Yennamalli <ymr79in at yahoo.co.in> wrote:
> Hi all,
> A query related to rerunning MD. 
>For eg: After 5ns run of MD I need to rerun from 3ns
> and I take the structure closest to it from the
> trajectory files. Taking this 3ns.gro as the starting
> structure I redo all the steps for preparation. In
> such a case, I am assuming that the velocity will be
> taken into account and I need not generate velocity
> again. 
> Am I right?

It depends why you want to rerun.
1) you lost the trajectory and need to regenerate it: then
you'd need to get the more exact continuation run possible.
tbpconv -f traj.trr -time 3000 -e ener.edr -s topol.tpr -o continuation.tpr

2) you just want to run an alternative route: then the way
you describe is fine. Generate new velocities (gen_v in mdp file)
and run grompp in the usual way using the 3ns.gro.

3) you need to rerun the existing trajectory: then you need tp
generate a new mdp file where you make sure to "only" modify
the frequency of energy writing (nstenergy= 1) and the update of
the lists (nstlist = 1). Use the trr file.
The command should be something like:
mdrun -rerun rerun.trr -s rerun.tpr

> Regards,
> Raghu
>      Forgot the famous last words? Access your message archive online at 
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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