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

[Justin Lemkul]

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. 
That's useful.

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

-- 
==================================================

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

==================================================