VMD-L Mailing List

From: Sebastian Maximilian Wilhelm (Sebastian.Wilhelm_at_rwth-aachen.de)
Date: Tue Mar 08 2011 - 05:21:10 CST

Hi,

I am wondering about two different calculated results for the electrostatic energies between two atom sites:

If I am calculating the electrostatic energy via 'measure energy elect {123 124} q1 -0.82 q2 0.41' directly in the VMD console, I receive a value, which I can reproduce manually with a relative dielectric epsilon_r = 1. I know, that this assumption (epsilon_r = 1) isnīt physically correct, especially if there is a great distance and thus probably other molecules between index 123 and 124.

Anyway, if I calculate the same type of energy via NAMDenergy between index 123 and 124 with the same charges as above and the initially loaded values for cutoff-distance = 12 and dielectric = 1, the result differs from the result of VMD, especially for great distances between the analyzed indices. The absolute values of the results are always smaller than the absolute ones from VMD.

To me, the only difference between these two calculation methods (U1=q1*q2/(4*pi*epsilon0*r) and U2=epsilon14*C*q1*q2/r (NAMD Userīs guide)) is the epsilon14. I calculated the ration between U1 and U2 in order to get the epsilon14. The result was: the greater the distance between index 123 and 124, the smaller the epsilon14 and thus the U2. But in the Userīs guide is written, that the epsilon14 has to be a constant.

My question is: why is there a difference between these two methods and which one would you recommend?

By the way: the calculation of vdw-energies via 'measure energy vdw {123 124} rmin1 ... rmin2 ... eps1 ... eps2 ...' and NAMDenergy always produce the same results.

I will appreciate your answer!

Best regards,
Sebastian