Re: [AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF?

From: <>
Date: Fri, 25 Mar 2011 04:25:37 -0400 (EDT)


> Could you mind to let me know the command used in ptraj to calculate the
> histogram P(x)? Once we got the P(x), should we use wham or any other
> program to calculate the dF=-RTlnP(x)?

ptraj would give you just the time series of values. Any data analysis
program (xmgrace, grace, origin, etc.) will build a histogram from it and
will require user decisions on e.g. how fine grained it should be.
Transforming your bin-likelihood into dF can be done by hand or in
gnuplot, origin, calc and even, dare I name it, Excel...


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Fri Mar 25 2011 - 01:30:03 PDT
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