On Mon, 28 Jan 2008 08:57:47 +0000 (GMT)
Ragothaman Yennamalli <[EMAIL PROTECTED]> 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
XAvier
Regards,
Raghu
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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