Re: energy calculation with namdenergy

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Sep 05 2018 - 08:18:56 CDT

I've not personally used namdenergy for this purpose, but what you describe
sounds reasonable. The force field energy scale is completely arbitrary and
absolute energies very rarely correspond to a physically meaningful
quantity. You might consider creating a reference system and then
subtracting out that energy or else check the literature for how hydrogen
bond energies have been measured in the past.

HTH,
BKR

On Wed, Sep 5, 2018 at 8:33 AM Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> Dear all,
>
> I calculated energy of hydrogen bonds between atoms of a protein using
> namdenergy function. This is the command I used in my tcl script.
> set mol [mol new mypsf.psf type psf waitfor all]
> mol addfile mydcd.dcd first 0 last -1 waitfor all molid $mol
> set $atom1 [atomselect $mol "index 1"]
> set $atom2 [atomselect $mol "index 2"]
> set energy [namdenergy -nonb -sel $atom1 $atom2 -par myparameterfile.inp
> -updatesel]
>
> the script calculates energy and gives an output of a list with each
> element having 6 values. As I know these 6 values are corresponding to
> {molecule frame vdw elec totalnonb total}
>
> However, the values I get as energy of H bonds are extremely higher than
> the energy of typical H bonds. I would like to know whether there is
> something wrong in my code or is it required to correct the values some way
> to get the correct energies.
>
> Thank you.
> Best regards,
> Monika
>
>
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
>

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