[gmx-users] Pushing the pulled ligand into the binding pocket

Justin Lemkul jalemkul at vt.edu
Wed May 6 13:44:19 CEST 2015

On 5/6/15 3:59 AM, Ayesha Fatima wrote:
> Dear Gromacs users,
> I have just started using gromacs 5.0.4 for steered dynamics and am running
> a setup for pulling my ligand out of the binding pocket. It is still
> running but a few questions to the users since this method is being used
> very frequently.
> 1) I have pulled my ligand in the +z direction but used the
> pull_geometry=distance. Now to push it back into the pocket what should be
> the code? Is it the same or i have to to use pull_geometry=direction and
> give a direction vector? I checked the mailing list but could not find a
> satisfactory answer.

You can do it with any method.  If you want to use distance, use a negative pull 
rate.  If you want to use direction, use a negative pull vector.



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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