scripts for binding free energy calculation using SMD and Jarzynski's equality

From: Marc Q. Ma (
Date: Wed Aug 17 2005 - 09:45:12 CDT

Dear VMD and NAMD users/developers,

Does anyone have a script for the binding free energy or potential of
mean force calculation using SMD trajectories (reversible or
irreversible pulling) and Jarzynski's equality, as demonstrated in Park
et al. 2003 in JCP? We are using SMD to study the unbinding pathway of
a family of ligands in complex with an enzyme. We would appreciate it
so much if anybody would like to share such a script with us.


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