[gmx-users] Re: mdrun -rerun and box size bug not fixed?

Berk Hess gmx3 at hotmail.com
Tue Nov 6 14:33:43 CET 2007

>From: Michel Cuendet <michel.cuendet at isb-sib.ch>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Re: mdrun -rerun and box size bug not fixed?
>Date: Tue, 06 Nov 2007 14:12:29 +0100
>I think I got it :-) Using gmx 3.3.1 with the same thermostat and barostat 
>settings as the original run, I get the right LJ energies within 0.1%. I 
>used tcoupl and pcoupl = "no" because I somehow remembered that thermostats 
>could do weird things when rerunning (see the old thread : 
>http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html )
>But apparently the box is not reread form the trajectory if the pcoupl 
>option is deactivated. It would be much safer for users if the appropriate 
>options were automatically set when -rerun in invoked:
>nstlist = 1
>nstenergy = 1
>NO rescaling of velocities
>NO rescaling of box size
>Do read the box sizes from the trajectory

The box is read, but in several parts of the code there are optimizations
for fixed box dimensions (i.e. no pcoupl, no deform).
This is indeed a bit tricky, but I don't know if we would want to change 
for the rerun option.

We do want scaling of velocties, since this influences the kinetic energy,
also for reruns.

Neighbor searching is already performed every step, independent of nstlist.
We could consider using nstenergy=1 for rerun, but I think that currently
you should already get the energy as often as for the original run, unless
you use a trajectory without step numbers (e.g. pdb).


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