[gmx-users] Umbrella sampling tutorial

[Justin Lemkul]

On 10/7/16 4:41 AM, gozde ergin wrote:
> Dear all,
>
> I would like to ask a question about Justin’s tutorial. By using the
> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
> effect of this restraint removed during the WHAM?
>

Not to my knowledge, no.  The restraints in the tutorial are there to mimic the 
fact that there are only five peptides, when in reality, there are millions, so 
the effects of the forces are quite different in vitro/in vivo.  Restraining one 
peptide makes the remaining four peptides more stable, more realistic.  WHAM 
doesn't do anything to change this.

> I want to do a similar thing by applying restraint force on the organic
> molecule on the bulk water in order to inhibit their movement inside the
> bulk. Should I consider the removing of the restraint in PMF?
>

In the case of freely diffusing molecules, I suspect such a restraint would have 
a much more profound impact.  Why do you want to do this?

-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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