Subject: Re: Parameterization

From: Howard Alper <[email-masked]>
Date: Wed, 16 Sep 1998 12:59:43 -0500

Hello,

  I'm sorry if this is a repeat, but as far as I could tell this message
did not post when I originally sent it - twice.

  Several weeks back I wrote about parameterization and units in
simulation (still waiting for some replies...)  Now I have some
questions about parameterization to create forcefields for MD
simulations.

  Specifically, I am interested in parameterizing Nitromethane.
While any information regarding a set of parameters (bond, angle,
torsion, out-of-plane,charges,van der Waals, etc) would be welcome,
we are interested in generating the neccesary parameters, and in a form
suitable for use in CHARMM.  To this end I have several questions:

1) I need to derive, somehow, structural parameters and force constants
for bond-stretching and angle-binding.  The force constants should
be in units of energy/(angstroms**2) and energy/(radian**2) (I have
seen some force constants in old papers that give force constants
in units of millidynes/angstroms, but I do not understand how that
relates to the case of angle-bending constants...)  I can perform
an optimization and frequency calculation in Gaussian, for example, but 
from what I can tell the resulting frequencies and force constants
are for the normal modes of the molecule, not bonds and angles/etc.
Does anyone know if Gaussian has any options to derive the type of
force constants I require?  Or, does anyone know of a post-Gaussian
analysis program that would do the above?

2) I also need to derive van der Waals parameters.  One person I asked 
said something on the order of "you can derive that from the interaction
of two nitromethane molecules".  To a parameterization novice, that is
not very specific advice.  Could anyone clarify what in detail needs to
be done, provide references, describe how programs like Guassian might
be used to get VDW parameters, etc?  (If one calculates the interaction
energy of two nitromethane molecules at verious distances and
orientations, is not the total energy for a configuration the sum
of coulombic and VDW terms?  Does that mean the charges must first
be derived?)

  Thanks in advance,

  Howard Alper

-- 

Howard E. Alper, Ph.D.
Dept. of Chemistry and The Advanced Materials Research Institute
University of New Orleans
New Orleans, LA 70148
504-280-7216

 - Helping molecules find happiness for almost a 5th of a century.