[gmx-users] Umbrella pulling Drug + Ion channel

[Justin Lemkul]

On 3/26/14, 1:52 PM, Andres Ortega Guerrero wrote:
> 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?
>

It sounds like you're mixing up the purposes of pull_group0 and pull_pbcatom0. 
Distances are calculated relative to pull_group0, which is the reference group.

-Justin

>
> 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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>   		 	   		
>

-- 
==================================================

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

==================================================