[gmx-users] pcoupl Berendsen

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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