[gmx-users] Umbrella pulling Drug + Ion channel

[Andres Ortega Guerrero]

Thank you Justin , 

In my case i could get the geometries with this pull code, but, 
mi pull_pbcatom0, is in the middle of the ion channel pore, 
shouldn't i get positive and negatives distances ligand crossing this atom?
because i am getting distances as the center of the whole protein
or should i repeatthe pull code , and instead of protein, use 4 residues ( my channel has 4 chains)
in the middle of the pore?


Thank you Justin 

> Date: Tue, 25 Mar 2014 12:32:24 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Umbrella pulling Drug + Ion channel
> 
> 
> 
> 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
> >   		 	   		
> >
> 
> -- 
> ==================================================
> 
> 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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