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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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