[gmx-users] pcoupl Berendsen

[Dallas Warren]

> 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.

https://twitter.com/dr_dbw/status/968624615063937025

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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.