[gmx-users] Re: gmx-users Digest, Vol 15, Issue 6

[Berk Hess]

>From: Pim Schravendijk <schraven at mpip-mainz.mpg.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Re: gmx-users Digest, Vol 15, Issue 6
>Date: Tue, 5 Jul 2005 14:59:46 +0200 (CEST)
>
>
> > Date: Mon, 04 Jul 2005 11:18:54 -0400
> > From: Brian Stephenson <bcstephe at MIT.EDU>
> > Subject: [gmx-users] restarting runs
> >
> > Hi all,
> >
> > ...
> >
> > I've  noticed things like this using GROMACS before--when I restart runs
> > using my old output as my new starting point,
> > the initial behavior seems unequilibrated.
> >
> > ...
> >
> > Any suggestions will be much appreciated!
> >
> > Thanks,
> > Brian
>
>Do you use pressure coupling? It might have to do with your coupling
>starting unequilibrated.
>
>You coulda avoid this by, when you restart a run, doing this by using
>tprconv and use the last complete frame from your .trr file and .edr file.

I don't think this it the problem.
It would only have a very minor effect on the system,
which you can not observe directly, only by comparing with an exact
continutation run.

My first guess would be that the same starting coordinates or velocities
have been used.

And it the simulations true md, or sd or bd?

Berk.