Re: calculating non bonded energy using namdenergy

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Sep 20 2018 - 09:49:14 CDT

1. As long as you get energies out of NAMD, you are using the namdenergy
plugin correctly. Unfortunately, the MD engine (NAMD) and the force field
(you didn't specify which one) do exactly as they are told, and compute the
energy of the configuration you give as it is. It is up to you to provide
a structure that is geometrically reasonable for the given force field.
For example, if you have any two atoms that are too close, the repulsive
term of the LJ potential will dominate everything.

2. To compute the force between any two atoms, you could either (1) look up
the force field parameters yourself and use a pocket calculator, or (2)
differentiate the expression of the potential (LJ or Coulomb) with respect
to *r* to get the expression for the force, then use the value of the
energy and the value of *r* (which you know) to get the coefficients. This
is best done if you run namdenergy on the vdW and electrostatic parts
separately.

3. If this is a question about the syntax of namdenergy, can you be more
specific and write down which is the expression that you think it returns,
and ask to confirm whether it's the correct one?

On Wed, Sep 19, 2018 at 11:30 PM Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> 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
> -updatesel]
>
> 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,
> Monika
>
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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