energy calculation with namdenergy

From: Monika Madhavi (
Date: Wed Sep 05 2018 - 07:32:00 CDT

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

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,

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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