[gmx-users] Umbrella pulling Drug + Ion channel

[Justin Lemkul]

On 3/25/14, 8:15 AM, Andres Ortega Guerrero wrote:
> Yes during Equilibration, the drug and the channel was restraint, yesterday , i tried changing the pull_geometry to position
> and it worked, i think that maybe there was problem with my cylinder configurations , this was my position configuration,
> considering this, i might think that theres not a problem of stability could be this true?
>

Likely something was wrong with the cylinder pull settings, yes.  But if you 
accomplished what you needed with position, then I suspect it's not very 
worthwhile to dissect what that problem was.

-Justin

> thank you Justin in advance
>
> ; Pull code
> pull            = umbrella
> pull_geometry   = position  ;
> pull_vec1       = 0.0 0.0 1.0 ;
> pull_start      = yes       ; define initial COM distance > 0
> pull_init1             = 0 0 0
> pull_ngroups    = 1
> pull_group0     = Protein
> pull_group1     = DOX
> pull_rate1      = -0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
> pull_pbcatom0   = 8485
>
> Andrés
>   		 	   		
>

-- 
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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 601
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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