Re: energy calculation with namdenergy

From: Brian Radak (
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.


On Wed, Sep 5, 2018 at 8:33 AM Monika Madhavi <>

> 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.

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