[gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?

[Justin Lemkul]

On 8/27/15 12:30 PM, Victor Ma wrote:
> hello,
>
> I tried various setting of the pull code. But my ligand stays there
> intact!!! Here is my pull code:
> pull            = umbrella
> pull-dim        = Y Y Y
> pull-start      = yes       ; define initial COM distance > 0
> pull-ngroups    = 2
> pull-ncoords    = 1
> pull-coord1-groups   = 1 2
> pull-group1-name     = Site
> pull-group2-name     = LIG
> pull-coord1-rate      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull-coord1-k         = 1000      ; kJ mol^-1 nm^-2
> pull-geometry = direction-periodic
>
> Can anyone please give any suggestion?
> Thank you!!!
>

You need a negative pull rate to cause the ligand to approach the target site.

-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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