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

From: Gustavo Seabra <>
Date: Fri, 25 Mar 2011 09:33:18 -0300

Hi Catein,

Have you already decided which variables you are going to plot? A
protein has a **lot** of degrees of freedom, and you can plot at most
3 of them. Once you have that decided, you can use ptraj to give you
the value of those variables for every snapshot, then use any
graphical program such as Origin, Matlab, SigmaPlot, GnuPlot, etc. to
transform the data to a 3d-histogram.

Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417

On Fri, Mar 25, 2011 at 5:13 AM, Catein Catherine
<> wrote:
> Thank you All who tried to help.
> Yes. Thomas.  It is what I meant.
> I am trying to analysis the free energies landscape for a protein.  I have done 20ns simulation for the system.  The RMSD, energies, etc are converged.
> 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)?
> Best regards,
> Catherine
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Received on Fri Mar 25 2011 - 06:00:04 PDT
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