[gmx-users] Umbrella Sampling tutorial

Justin Lemkul jalemkul at vt.edu
Sun Dec 1 14:28:56 CET 2013

On 12/1/13 8:04 AM, shahab shariati wrote:
> Dear Justin
> Very thanks for your reply
> I will slow pulling by changing pull_rate1 from 0.01 to 0.001
> and pull_k1 from 1000 to 100.
> I have a basic question. Before minimization, where should I put drug
> molecule? into water molecules or into lipid bilayer? Should I put drug
> molecule in the specific position?

If you're trying to pull it into/across the bilayer, the most intuitive thing to 
do is place it within the water and pull it across to set up your 
configurations.  You can do it however you like.



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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