[AMBER] Regarding energy decomposition

From: aneesh cna <aneeshcna.gmail.com>
Date: Wed, 8 Dec 2010 07:40:17 -0500

Dear Amber users,

                 I am using Amber 9.0 for simulation. Using *ANAL* utility
in Amber I am trying to see the electrostatic interaction energy between the
two groups, say 1 and 2, contains residues which are not bonded to each
other. Anal will output the electrostatic energy matrix as shown below,
which is a sum of both 1-4 and non bonded interaction.

********************************************************************************************************************************************

  ELECTROSTATIC (N-B + 1-4) INTERACTION ENERGY MATRIX




            1 2 3
    1 -510.214 -120.865 -286.239
    2 -120.865 4.281 31.622
    3 -286.239 31.622 18.220

********************************************************************************************************************************************

   Is it right to include the 1-4 electrostatic interaction if I want to see
the interaction energy between two non-bonded groups? Is there any other way
to see just the non bonded interaction alone?



Thanks in advance


Sincerely
Aneesh
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Received on Wed Dec 08 2010 - 05:00:05 PST
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