[gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause

Ladasky blind.watchmaker at yahoo.com
Thu Sep 20 08:34:49 CEST 2012

Justin Lemkul wrote
> So the initial equilibration was NPT? 


Justin Lemkul wrote
> Did you ever try simply running NVT with 
> either Berendsen or V-rescale before applying any type of pressure
> coupling?

No, I haven't, and I don't remember seeing that described in any work flow.

Justin Lemkul wrote
> Immediate application of NPT is often unstable for a variety of reasons,
> not 
> necessarily the temperature coupling algorithm.

All right, that's useful information.  But what I am doing here is ripped
from a tutorial file, and modified as little as possible.  I try not to
change things that I do not yet understand.  My source for the MDP files was
the lysozyme tutorial shell script that accompanied GROMACS 3.3.  If there
are procedures in that tutorial that are obsolete, I guess I'm finding that
out the hard way.

Justin Lemkul wrote
> Anyone is welcome to contribute to the wiki; it is a community project,
> after 
> all.  I would also be interested to see if it can be demonstrated that NPT
> with 
> V-rescale + Berendsen is unstable after an independent NVT simulation with 
> either method.

I may take the time to try that experiment later.  I'll report back with any

Thanks for your help!

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