[gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 12/1/13 9:39 AM, shahab shariati wrote:
> Dear Justin
>
> Thanks for your reply
>
>
> If I place drug molecule within the water, can I use the same Pull code
> parameters in the case drug molecule within lipid bilayer?
>
> pull            = umbrella
> pull_geometry   = position  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = CHOL_DOPC
> pull_group1     = drg
> pull_rate1      = 0.001      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 100      ; kJ mol^-1 nm^-2
> pull_init1      = 0
> pull_vec1       = 0 0 1
>

Try it and see.  The settings depend on where you place everything.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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