Subject: Re: CCL:Thermodynamic corrections at MM level (fwd)

From: Anton Feenstra <feenstra~at~chem.vu.nl>
Date: Thu, 04 Dec 2003 18:30:05 +0100

Maciej Haranczyk wrote:

> Dear CCLers,
> 
> I did some DFT (B3LYP) calculations on small DNA fragments (~200atoms).
> I would like to calculate thermodynamic corrections (EZPV,H,G) for these
> systems but since I do not have fully optimized geometries (I had to
> freeze nucleic acid bases layers because B3LYP does not deal with
> dispersion (pi-stacking)) I cannot run frequency calculation at B3LYP
> level.
> I would like to calculate thermodynamic corrections with MM approach and
> then add it to B3LYP energies. Since I am not familiar with MM programs
> I would be grateful if someone suggested me any free program than can do
> that or paper on this topic.

I'm not sure if this answers your quistion, but in the MD package Gromacs
one can perform what is called 'Quasi Harmonic Entropy' calculations,
involving covariance analysis on atomic coordinates and analysis of the
resulting eigenvalues that correspond to generalized modes of motion (i.e.
the eigenvectors). Gromacs is available for free at www.gromacs.org.

There are more Gromacs users (and developers) on the CCL, so you may
also get (more appropriate) answers from them...?

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra~at~chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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