**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Thu Sep 20 2018 - 09:49:14 CDT

**Next message:**Rabeta Yeasmin: "Re: Bad structure after converting the coarse grained last frame to all-atom"**Previous message:**Vermaas, Joshua: "RE: Best water model"**In reply to:**Monika Madhavi: "calculating non bonded energy using namdenergy"**Next in thread:**Peter Freddolino: "Re: calculating non bonded energy using namdenergy"**Reply:**Peter Freddolino: "Re: calculating non bonded energy using namdenergy"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Rabeta Yeasmin: "Re: Bad structure after converting the coarse grained last frame to all-atom"**Previous message:**Vermaas, Joshua: "RE: Best water model"**In reply to:**Monika Madhavi: "calculating non bonded energy using namdenergy"**Next in thread:**Peter Freddolino: "Re: calculating non bonded energy using namdenergy"**Reply:**Peter Freddolino: "Re: calculating non bonded energy using namdenergy"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Mon Dec 31 2018 - 23:21:24 CST
*