[AMBER] calculate PMF in string methods

From: Chunli Yan <utchunliyan.gmail.com>
Date: Wed, 16 Aug 2017 19:42:03 -0400


After I finished the simulation by using string methods, I got a lists of
output file for each image (mdcrd*, rst*, stsm* and so on). In amber manual:

 When you get the biasing potential (*.nc file), you can always use the
nfe-umbrella-slice utility to access

its content and get a friendly-written ASCII file from which one can obtain
the free energy map. The output

is the free energy value, which is the opposite of the biasing potential (
f = 􀀀U (units kcal*=*mol )). The

nfe-umbrella-slice utility has been included in AmberTools.

Usage: nfe-umbrella-slice [options] bias_potential.nc

I am wondering how to compute free energy along the image. How to get the
biasing potential.



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Received on Wed Aug 16 2017 - 17:00:02 PDT
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