[gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

Soham Sarkar soham9038 at gmail.com
Sat May 19 19:38:14 CEST 2018

```Thanks for your reply Justin...
But these pressure I provided here are by doing the gmx energy -f energy.edr
And then selecting the pressure from the list. It only shows these values
for respective temperature windows after 1st stage of equillibration.. What
should I do?
How do I know what is the actual pressure of my system?
Or is there any pressure convergence protocol in REMD?
-Soham

On Sat, 19 May 2018, 9:11 pm Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 5/19/18 8:45 AM, Soham Sarkar wrote:
> > Thanks for reply.. but what is the actual pressure of the system? You
> > mentioned it as the instantaneous pressure
>
> Instantaneous simply refers to the value at any given time point; these
> will fluctuate wildly, particularly for a tiny system like yours, and
> the instantaneous values are meaningless.
>
> The average pressure (and its distribution) is more meaningful. Compute
> that with gmx energy.
>
> -Justin
>
> > On Sat, 19 May 2018, 6:03 pm Mark Abraham, <mark.j.abraham at gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> This is normal for instantaneous measurements of pressure. See
> >> http://www.gromacs.org/Documentation/Terminology/Pressure
> >>
> >> Mark
> >>
> >> On Sat, May 19, 2018, 13:04 Soham Sarkar <soham9038 at gmail.com> wrote:
> >>
> >>>   Dear All,
> >>> I have a small system including a 4 residue peptide. I have chosen 8
> >>> temperature windows for doing REMD simulation of this system. After the
> >>> temperature convergence of the 8 systems in the 1st stage of
> >> equillibration
> >>> run, the obtained pressure are quite absurd, which is not change that
> >> much
> >>> after the 2nd stage of production run. I want to know whether this type
> >> of
> >>> pressure range is ok for a system or not? Should I carry out analysis
> in
> >>> this pressure range? As in normal md simulation there is a pressure
> >>> convergence step which takes the system to the desired pressure. This
> >> type
> >>> of step is not there in the REMD simulation.
> >>> The pressure and temperature of this system after 1st stage of
> >>> equillibration of 10ns are as follows
> >>> Temperature(K) Pressure(Bar)
> >>> 350.112              -28.4761
> >>> 369.218             262.054
> >>> 389.201              592.84
> >>> 410.074             946.021
> >>> 429.12               1273.92
> >>> 448.873              1628.61
> >>> 469.438              2005.04
> >>> 490.272              2392.50
> >>>
> >>>
> >>> --
> >>> SOHAM SARKAR
> >>> Junior Research Fellow
> >>> Department of Chemistry
> >>> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
> >>> --
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> >>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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```