[gmx-users] PMF calculation

Za Pour za.pour at yahoo.com
Mon Aug 19 18:27:44 CEST 2013

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?
I appreciate your time and help.

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