[gmx-users] PMF and lack if NPT equilibration

[Justin Lemkul]

On 10/8/16 2:46 PM, Alex wrote:
> Dear gromacs user,
>
> In a PMF simulation of a short peptide on solid surface, I am using the
> "direction-periodic" as "pull-coord1-geometry" in the Z  direction, then as
> you know the equilibration of the system in NPT ensemble is not doable for
> the individual windows. So, for each windows of umbrella sampling, I am
> going to do minimization and NVT equilibration and then MD production. I
> was wondering if the lack of the NPT  equilibration would not badly affect
> on the result PMF? If so, how can I compensate it somehow?
>

All you're doing is sampling under a different ensemble.  There's no reason to 
think that a PMF requires an NPT ensemble.

-Justin

> By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns
> of production simulation of my initial system before coming to the pulling
> step.
>
> Thanks.
>
> Regards,
> Alex
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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