From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Apr 29 2010 - 02:59:42 CDT
Dear Yangdong,
> Based on the CHARMM22 force field, i use my own code to roughly minimize
> a peptide and compare each term of interactions with the results of
> minimization of namd2.6. My approachment is simply to set velocity zero
> everay step, which is inferior to annealing algorithm that namd may adpot.
>
> All interactions are comparable and consistent with the results of namd
> except for electrostatic interaction when dielectric constant is 1.0, the
> absolute value of which by my code is nearly twice as big as that by namd.
> As to VDW and Electrostatic interactions, all pairs of atoms without bond
> interaction( bond stress, angle bend, dihedral torsion, improper dihedral)
> are considered in my code. I did not use cut-off method. Can you find
> something wrong?
Maybe. In the CHARMM ff, the rule is to include nonbonded terms for
all atoms except those linked through one or two bonds (which will
typically be coupled by bond and angle terms). Atoms connected by a
torsion term (3 bonds) have their full nonbonded interactions (the
so-called 1,4-interactions). There are a few exceptions: for some atom
types, the CHARMM parameter files list modified Lennard-Jones
parameters for 1,4 interactions. Electrostatics is never modified,
though.
Cheers,
Jerome
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