[gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?
jalemkul at vt.edu
Sat May 19 19:41:07 CEST 2018
On 5/19/18 1:37 PM, Soham Sarkar wrote:
> 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?
gmx energy prints the average and standard deviation to the screen.
What you are getting are the "actual pressure" values of the system, but
what you have to understand is that just looking at those values
shouldn't lead you to conclude that there's anything wrong.
> Or is there any pressure convergence protocol in REMD?
The system has to have enough time to relax under the new ensemble, but
that's true of both temperature (which relaxes quickly) and pressure
(which does not). Most REMD is done with an NVT ensemble to avoid this
problem (and if you're already using NVT then you should stop worrying
about the pressure entirely).
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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