AMBER Archive (2008)

Subject: Re: AMBER: free energy

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Wed Jul 16 2008 - 11:22:45 CDT

Hi Boutheina,

there are several different answers depending on what 'the free energy
profile' is. If you want to follow a reaction coordinate you could use
Ambers umbrella sampling facilities. If the difference between two defined
end states is of interest, MM-PBSA might be the method of choice or for
small chemical changes, you could employ the thermodynamic integration
free energy methods. If you want to analyse a nonequilibrium free energy
profile using Jarcynskis equation, you could try out the jar/SMD
facilities. We need somewhat more information about your specific question
to help here.

Kind Regards,

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Wed, 16 Jul 2008, Boutheina Kerkeni wrote:

> Hi
>
> Does any one knows how to compute the free energy profile with Amber?
> Thanks
> Regards
> Boutheina
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