[gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 11/10/13 9:14 AM, shahab shariati wrote:
> Dear Justin
>
> Very thanks for your reply.
>
>> What you described earlier should not be attempted with "distance"
>> geometry. It won't work very well. The use of restraints is almost
>> NEVER necessary, especially in the case where the reference group > is
> much more massive than the pulling group.
>
> I want to calculate Potential of mean force as a function of the distance
> between the centers of mass of drug and the lipid bilayer.
>
> You said distance geometry won't work very well in my case.
>
> What is your better suggestion about my case?
>

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html

pull_geometry = position

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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