NAMDenergy electrostatic energies

From: Sebastian Maximilian Wilhelm (
Date: Mon Feb 28 2011 - 10:41:03 CST


I am trying to compute all intermolecular energies of my system (for beginning just water). The calculation of vdW-energies works very well, but I have problems with the values for the electrostatic energies.

In the NAMD 2.7 userīs guide, in the chapter 'force field parameters - nonbonded potential energy terms' is written, how NAMD calculates the vdW- and the electrostatic energies. I am a little bit confused about equation (7): since C=1/(4*pi*epsilon0), epsilon0 would be regarded twice in eq (7), but in all physic books I looked up, there is written U=Q1*Q2/(4*pi*epsilon0*r), with epsilon0 only regarded once in the denominator. Which formula do I have to use?

Besides, I tried both formulas, but I didnīt receive the value NAMDenergy has calculated. I converted Angstrom into meters for the distance r and both partial charges Q1 and Q2 into coulomb. The result of the calculation of U with SI units is J, but even after conversion into kcal/mole (which is the unit of vdW-energies), this result doesnīt fit to the NAMDīs one.

I thank you for your help!

Best regards,
Sebastian Wilhelm

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:41 CST