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

From: Mahmoud Soliman <>
Date: Thu, 24 Mar 2011 18:06:25 +0200

   Thanks David, I will look through the manual!
   Best wishes
   On 3/24/11 5:44 PM, David A Case wrote:

On Thu, Mar 24, 2011, Adrian Roitberg wrote:

You can do umbrella sampling in amber using restraints

I do not think we have a tutorial for that, but if you read on umbrella
in general, it should be simple to see how you use restraint potentials
to do it in amber.

Just to add to Prof. Roitberg's comments: there is a section (4.2) in the
Users' Manual on "umbrella sampling", with sample inputs. See also Section


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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 - 09:00:08 PDT
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