[gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?
soham9038 at gmail.com
Sun May 20 16:15:17 CEST 2018
Thanks for clarification..
On Sat, 19 May 2018, 11:11 pm Justin Lemkul, <jalemkul at vt.edu> wrote:
> 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
> > And then selecting the pressure from the list. It only shows these values
> > for respective temperature windows after 1st stage of equillibration..
> > 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 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
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