Subject: Re: CCL:eisai monos ?diabase to (fwd)

From: Rick Venable <[email-masked]>
Date: Fri, 26 Mar 1999 12:10:45 -0500 (EST)

On Fri, 26 Mar 1999, I. Kerkines wrote:
> a)I am interested in finding a program (in C or better
> in Fortran), that from classical trajectory calculations
> via Molecular Dynamics, is able to calculate the Raman
> or/and Rayleigh spectra of a mixture not necessary
> composed of monoatomics.

CHARMM can perform quasiharmonic anaylis of MD trajectories, essentially
determing modes of motion from the simulation data.

> b)In MD we use the term "Potential Energy".Which experi-
> mental quantity is very close to it and so we can
> compare with it when  we work in the GAS phase with
> pure substances or mixtures of diatomics molecules.

The MD potential is relative enthalpy-- meaning you can reasonably
compute enthalpy differences, but you shouldn't trust the absolute value
of the potential energy; it's different for different MD parameter sets. 

> c)When we have to work a mixture we usually apply 
> the well-known Lorentz-Berthelot rules.But it is not
> too accurate.Is there any general procedure when we
> have excess properties(enthalpy,volume) to calculate
> a more accurate interaction L-J potential between the
> dissimilar species of a mixture? 

CHARMM can evaluate energetic between arbitrary sets of particles, using
just the VDW term in the potential, if that's what you mean.

CHARMM is not freely distributed, but is available for academic license
to the mostly Fortran source code for a few hundred dollars U.S. from
Harvard Univ.; see

	http://yuri.harvard.edu

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]  |    \  /  |=|    position of the FDA; for that,
http://www.erols.com/rvenable       \/   |=|    see   http://www.fda.gov  )