[gmx-users] umbrella sampling tutorial

[Justin Lemkul]

On 3/17/15 9:06 PM, Ming Tang wrote:
> Hi Justin,
>
> Thanks a lot. I can move forward now.
> Recently, I am trying to pull  a triple helix, and want to fix the center of mass of the three terminal atoms. One paper said that it can be done by means of a strong harmonic restrain with a super large spring constant in Gromos96 53 a6. But I still don't know how to do this.  Can you give me some advice?

Absolute restraints can be used in the pull code, but I've never done it.  Note 
that such an approach is incompatible with NPT.  Freezing may also be an option, 
but then you're acting directly on all the atoms and frozen groups carry their 
own artificiality.

-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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