[gmx-users] Umbrella sampling

[Justin Lemkul]

On 9/5/16 3:16 AM, masoud aliyar wrote:
> Hi everybody
> I’m trying to do Umbrella Sampling by using Justin’s tutorial. Everything
> is ok but some aspects of the procedure remain a bit unclear to me. Why
> don’t we need to do NVT equilibration before first MD? And why pull codes

Equilibrate however you like.  There is no one-size-fits-all method.

In this case, I don't think there is much value in an additional NVT simulation 
because the starting snapshots are from a previous dynamics run (the SMD).

> are applied during NPT equilibration of selected windows or extracted
> frames?

Apply the conditions you would during simulation.  You can restrain via normal 
position restraints, but those allow deviations in the initial absolute 
positions.  If those allow sufficient variation, then the pull code has to do a 
large amount of work in the initial time steps, which can be unstable or 
otherwise undo some of the work of equilibration.

-Justin

-- 
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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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