**From:** Peter Freddolino (*petefred_at_umich.edu*)

**Date:** Thu Sep 20 2018 - 11:13:50 CDT

**Next message:**Peter Freddolino: "Re: Bad structure after converting the coarse grained last frame to all-atom"**Previous message:**Rabeta Yeasmin: "Re: Bad structure after converting the coarse grained last frame to all-atom"**In reply to:**Giacomo Fiorin: "Re: calculating non bonded energy using namdenergy"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Just one quick addendum on point 2 -- namdenergy does permit direct

calculation of forces between two atom groups by using the "Show Force

Output" check box or the -keepforce flag in the text interface.

Best,

Peter

On Thu, Sep 20, 2018 at 10:49 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>

wrote:

*> 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
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*> 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
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*>> 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:**Peter Freddolino: "Re: Bad structure after converting the coarse grained last frame to all-atom"**Previous message:**Rabeta Yeasmin: "Re: Bad structure after converting the coarse grained last frame to all-atom"**In reply to:**Giacomo Fiorin: "Re: calculating non bonded energy using namdenergy"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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