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

From: Mahmoud Soliman <>
Date: Thu, 24 Mar 2011 17:23:10 +0200

   Dear Thomas,
   Actually your reply to Catherine has encouraged me to seek your advice about
   my case: I need to do a PMF for some reaction coordinate (nucleophilic
   attack) using QM/MM facility in Amber 10. I read through steered MD
   simulation but it sounds to me (from the comments I get from Amber
   users/developers) that SMD is a bit doggy and some people getting some
   trouble to publish work with SMD. Is there any EASY and reliable alternative
   in Amber 10 that I can apply to do a PMF for NU or PT reactions in enzyme???
   do you have any tutorial/example for the methode you explain below to
   Catherine that I can use??
   Best wishes
   On 3/24/11 5:04 PM, [1] wrote:


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,
AMBER mailing list

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

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   Mahmoud E. Soliman

   Computational Chemistry & Modeling (PhD)

   Department of Chemistry

   University of Bath


   BA2 7AY

   United Kingdom




   Mahmoud E. Soliman

   Lecturer of pharmaceutical organic chemistry

   Pharmaceutical Organic Chemistry Dept.

   Faculty of pharmacy

   Zagazig University









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Received on Thu Mar 24 2011 - 08:30:04 PDT
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