calculating non bonded energy using namdenergy

From: Monika Madhavi (
Date: Wed Sep 19 2018 - 22:19:16 CDT

Dear all,

I used namdenergy to calculate non-bonded energy between two atoms using
the following command.
set energy [namdenergy -nonb -sel $atom1 $atom2 -par myparfile.inp

The values I get from this are very high compared to the expected values.
Therefore, I have few questions:
1. Does the syntax I used is correct?
2. Does the output of namdenergy is the potential energy or the force
between two atoms? If we want to calculate the force between two atoms,
what is the command to use?
3. When calculating non-bonded energy using namdenergy, should we divide
the value we get by 2 to get the correct interaction energy?

Any insight is greatly appreciated.
Thank you.
Best regrads,

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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