AMBER Archive (2005)

Subject: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion.

From: Pavan G (pavanamber_at_gmail.com)
Date: Sun Nov 27 2005 - 21:14:48 CST

Hello all,

I am trying to reproduce the value of EELEC for the first time step
recorded in a md run:
" NSTEP = 100 TIME(PS) = 1626.100 TEMP(K) = 298.76 PRESS = -18.6
        Etot = -76468.3208 EKtot = 35432.1212 EPtot = -111900.4421
        BOND = 22540.2259 ANGLE = 2334.1316 DIHED = 2373.1196
        1-4 NB = 749.3074 1-4 EEL = 24187.2168 VDWAALS = 20399.8387
        EELEC = -184484.2821 EHBOND = 0.0000 RESTRAINT = 0.0000
        EKCMT = 10710.9469 VIRIAL = 10864.5298 VOLUME = 383436.0683
        Density = 1.0553
        Ewald error estimate: 0.3583E-05"

This is a run containing ~40,000 atoms. I got the charges of the atoms
from prmtop file and distances using the coordinates of the mdcrd
file. Now, the crudest way I could calculate the Electrostatic
interaction is to pick 2 atoms from the 40,000 and calculate energy
using
E = charge.1 * charge.2 / distance
REF: http://amber.scripps.edu/Questions/units.html
But this obviously includes atoms which are covalently bonded and have
hydrogen bonds.
This gives me a number which is ~12 times the number by amber(EELEC =
-184484.2821).

Now, where is the mistake. What set of atoms should I consider/not consider ?

Thanks a lot
Pavan
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