Re: calculating non bonded energy using namdenergy

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Sep 20 2018 - 11:13:50 CDT

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
> 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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