VMD-L Mailing List

From: Rajitha Tatikonda (sairam.tatikonda_at_gmail.com)
Date: Wed Nov 07 2012 - 06:52:20 CST

Hi,

I have calculated dihedral energy using namdenergy plugin for a given set
of atoms of a given residue and the output values are quite different from
the one that I calculate it either manually or using tcl (measure energy
dihed ) . The one calculated manually or using measure energy dihed are
approximately same.
The following are the values that I got
manually 0.09076535669271901 kcal/mol
measure energy dihed 0.09076541662216187 kcal/mol
namdenergy plugin +1.9719 kcal/mol

Can someone let me know the probable reason behind this large deviation in
the energy magnitude using namdenergy plugin ? or am I lagging in
understanding what actually dihed in namdenergy plugin calculates ?

Any help will be highly appreciated.

Thanks in advance.

Regards,
Rajitha.