[gmx-users] Forced adsoprtion and desorption of a protein on a surface

[Justin Lemkul]

On 4/9/15 2:45 AM, James Lord wrote:
> Dear Users,
> I am wondering if anyone can help me out with forced adsorption/ desorption
> of a protein on surface. I am aware of pulling code in Justin's tutorial
> but that is not what I am looking for. I want a simple constant force
> (perpendicular to the surface) method to push and/or pull the protein
> (center of mass) onto /or from a surface at specific time intervals during
> the simulation . Appreciate any comments.

There's no way to tell mdrun to apply the pull code only during given time 
intervals, so you'd have to run for some time, create a new .tpr that contains 
pulling instructions to continue while applying the biasing potential, turn off 
the pull code or change it, repeat as needed.

-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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