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

[James Lord]

Thanks heaps mastermind Justin.
James

On Thursday, April 9, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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