[gmx-users] Umbrella pulling Drug + Ion channel
jalemkul at vt.edu
Tue Mar 25 17:34:03 CET 2014
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.
> 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
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
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