RMSD based PMF calculation with umbrella sampling

From: Wang, X. Y. (jeffwang20_at_gmail.com)
Date: Thu Dec 22 2016 - 04:26:21 CST


I want to do PMF calculations based on umbrella sampling sing RMSD as the
order parameter, but I found the tutorial not so clear and there is no
example. I am just starting to do free energy calculations and not familiar
with NAMD setup. Would you kindly share an example of the .conf and .in
file showing how to set up colvar? Thank you very much.

Dr Xingyong Wang
Vice-Chancellor’s Postdoctoral Research Fellow
School of Chemistry
University of Wollongong NSW 2522, Australia

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