Re: [AMBER] How to get the free energy landscape from a MD simulation?

From: <>
Date: Thu, 24 Mar 2011 11:04:03 -0400 (EDT)


I am not sure if this is what you mean, but if you can define a clear
reaction coordinate x for the change you see, e.g. some distance, you can
use ptraj to analyse the time series of movement along it, compute a
histogram P(x) and transform it into a potential of mean force via dF=
-RTln P(x). This is only meaningful if all points along x are well sampled

Kind Regards,


On Thu, March 24, 2011 10:55 am, Catein Catherine wrote:
> Dear Sir/Madam,
> I have done the MD simulations. I would like to analysis the free energy
> landscapes of a conformational change during a long MD simulations.
> Can I do it with ptraj or any other softwares or scripts?
> Best regards,
> Catherine
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Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Mar 24 2011 - 08:30:03 PDT
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