[gmx-users] Umbrella pulling Drug + Ion channel

Justin Lemkul jalemkul at vt.edu
Thu Mar 27 02:02:54 CET 2014

On 3/26/14, 8:58 PM, Andres Ortega Guerrero wrote:
> Thank you Justin
> i was wondering if you could, help with the doubt of the use of group0: i
> will use the entire PROTEIN but considering that the COM  is not in the
> middle of the ion channel's pore , and the PMF of the ligand crossing the
> pore, i assumed that this distances doesn't affect my calculations, because
> the internal n and c terminal dont interact with ligand, and in this case it
> is just a interpretation of the results problem? am i right

No.  The COM of the chosen group is used for calculation of the applied force. 
If the groups are chosen poorly, it will be reflected in the outcome.  If you 
want to study movement of a molecule through a pore, the reaction coordinate 
should reflect that direction and the groups chosen to suitably define that 
reaction coordinate.



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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