[gmx-users] umbrella simulation -pulling in other directions

[Justin Lemkul]

On 2/21/16 8:28 AM, Nikhil Maroli wrote:
> Dear all,
> i am doing Umbrella sampling,as my ligand is in x axis after i made a
> box,so i have to pull it towards -x direction instead of z which mention in
> tutorial, can i give
> pull_coord1_rate        = -0.01
> negative rate? is it make any sense or is there any ohter method to pull in
> -X direction
> i have attached an  image,waiting for the valuable suggestions!!
>

A negative pull rate causes the COM distance between the pulled and reference 
groups to decrease over time.  It does not necessarily dictate the direction 
along an axis in which the pulled group will move.  To pull along -x you need to 
set pull-coord1-vec appropriately.

-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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