[gmx-users] PMF calculation
za.pour at yahoo.com
Mon Aug 19 18:27:44 CEST 2013
Iwould like to calculate the PMF between two nanotubes covered
with some molecules. To do that, one nanotube has to be held fixedly and
is supposed to be moved as a rigid entity. To generate configurations, for fixed nanotube
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?
I appreciate your time and help.
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