[gmx-users] Umbrella sampling tutorial - V-rescale or Berendsen thermostat

[Justin Lemkul]

On 11/18/15 11:37 AM, Martin Nors Pedersen wrote:
> Hello everyone
>
> I am following the Justin Lemkul's tutorial for Umbrella sampling:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
>
>
> I am at the step where i want to perfom the NPT equilibration. Using the input
> file provided in the tutorial, I use grompp to prepare the .tpr file. I get a
> note, however, which states that the selected thermostat in the provided npt.mdp
> is not optimal:
>
>      " The Berendsen thermostat does not generate the correct kinetic energy
>       distribution. You might want to consider using the V-rescale thermostat. "
>
> I just want to ask if there is some specific reason for choosing the Berendsen
> thermostat over of the V-rescale in the NPT equilibration? According to the
> manual ( http://manual.gromacs.org/online/mdp_opt.html#tc ), they are similar
> except for a stochastic term which makes the V-rescale thermostat better. But I
> do not know if this has any (significant) influence in the NPT equilibration.
>

For equilibration, it doesn't matter.  Berendsen relaxes extremely quickly, so 
it is often used in initial equilibration.  V-rescale works fine, too.  Just 
don't use Berendsen for actual data collection.

Since the tutorial was derived from one of my published papers, I stuck with the 
actual input files/algorithms that we used back then.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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