# [gmx-users] pcoupl Berendsen

Dallas Warren dallas.warren at monash.edu
Fri Nov 9 02:16:55 CET 2018

```> A pressure without an error bar is a meaningless value. The fluctuations
> of pressure in most systems are on the order of tens or hundreds of bar,
> meaning your result is indistinguishable from the target value.

To help illustrate this, here is one example of the type of pressure
fluctuation you can get.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Fri, 9 Nov 2018 at 00:01, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 11/8/18 7:50 AM, Gonzalez Fernandez, Cristina wrote:
> > Dear Gromacs users,
> >
> > In my simulations, I have specified ref_p= 1bar but after MD simulation I obtain pressures equal to 0.19 bar (even
>
> A pressure without an error bar is a meaningless value. The fluctuations
> of pressure in most systems are on the order of tens or hundreds of bar,
> meaning your result is indistinguishable from the target value.
>
> > with long simulation times) when using pcoupl=Parrinello-Rahman. I know that Parrinello-Rahman is recommend for production runs and Berendsen for NPT equilibration. However, I have read in an article that Parrinello-Rahman is not stable for low pressures, so in such situations its better to use Berendsen. I have tried to use Berendsen for
>
> I would be interested to know how this "not stable for low pressures"
> was determined, because it seems completely unlikely to be true. Most MD
> simulations nowadays use Parrinello-Rahman for pressure coupling at 1
> bar/1 atm without any issue if the system is properly equilibrated (and
> if not, the problem is with preparation, not the barostat itself).
>
> > MD simulation but I obtain this Warning and I cannot remove it with the -maxwarn option.
> >
> > "Using Berendsen pressure coupling invalidates the true ensemble for the thermostat"
> >
> >
> > How can I use Berendsen for MD simulation?
>
> Simply, you can't, and you shouldn't. The Berendsen method produces an
> invalid statistical mechanical ensemble. It relaxes systems quickly and
> is therefore still useful for equilibration, but should never be
> employed during data collection. Full stop.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
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```