[gmx-users] Berendsen and Parrinello-Rahman

[Justin Lemkul]

On Mon, Dec 16, 2013 at 3:19 AM, Mahboobeh Eslami <
mahboobeh.eslami at yahoo.com> wrote:

> hi all my friends
> i am studying protein-ligand complex by gromacs 4.6.3
> i see followingText in gromacs site:
>
> Berendsen is often the best algorithm for equilibration, because it is
> the most robust to the volume changes that might be expected during
> equilibration. However it does not generate the proper thermodynamic
> ensemble, so once the volume has stabilized, another method should be
> used to equilibrate into the right ensemble.
>
> can i use two NPT equilibration and can i use Berendsen
> andParrinello-Rahman for them?
> thanks for your help
>

Sounds reasonable.  That's basically what the manual is telling you.  I
often find the Berendsen barostat to be unnecessary, as NVT with the
Berendsen thermostat, followed by NPT with Nose-Hoover or V-rescale for the
thermostat and Parrinello-Rahman for the barostat is stable enough.  That
may not necessarily be the case every time, though, so one should not be
fooled into thinking there are absolute rules here.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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