[gmx-users] PMF calculation

Justin Lemkul jalemkul at vt.edu
Mon Aug 19 19:41:39 CEST 2013

On 8/19/13 12:27 PM, Za Pour wrote:
> Dear gmx-users
> Iwould like to calculate the PMF between two nanotubes covered
> with some molecules. To do that, one nanotube has to be held fixedly and
> another one
>   is supposed to be moved as a rigid entity. To generate configurations,  for fixed nanotube
>   I used
> position restraints in all directions and for rigid nanotube,  I used the combination
>   of distance restraint plus position restraint in y and z direction  ( x is myreaction coordinate)
> to keep the nanotube shape. My question is, after obtaining all configuration, can I use position
> restraint for both nanotubes in all directionsin umbrella sampling step or I should conduct this
> step in the same condition of generation of configuration step?

What would be the point of using an umbrella potential between two species that 
are already restrained by other means?  It accomplishes nothing.



Justin A. Lemkul, Ph.D.
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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