PMF via constrained dynamics in NAMD

From: satya work (
Date: Mon Aug 31 2009 - 09:01:43 CDT


What is the best way to set up constrained dynamics along a known reaction
coordinate to construct potential of mean force in NAMD? I want to constrain
a small molecule along the bilayer normal of a lipid bilayer and calculate
the PMF from water to bilayer center. I am running SMD calculations, but
also would like to use constrained dynamics if possible.


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