[gmx-users] Umbrella Sampling - Loop Motion

Justin Lemkul jalemkul at vt.edu
Tue Nov 11 13:38:02 CET 2014

On 11/11/14 6:21 AM, Michael Carter wrote:
> Hi,
> I am setting up an umbrella sampling simulation to analyse the motion of a loop within my protein system.
> I have set it up so that the pull groups are:
> 1 – the loop (residues 208-14)
> 2 – the protein (protein)
> However, when doing this my conformations which I generate in the md_pull step are very strained. Is this because I am also including the loop in the 2nd pull group (defined as protein)?

Possibly.  The normal setup would be that the two groups aren't overlapping. 
They can be part of the same molecule, but probably a more judicious choice is 
warranted here.



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


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