[Chimera-users] Dielectric constant

[Conrad Huang]

The minimization is done with MMTK (http://dirac.cnrs-orleans.fr/MMTK/) 
using steepest descent with Amber99 force field.  No options are 
specified for the force field.  According to MMTK documentation, that 
means: "no cutoff; inclusion of all pairs, using the minimum-image 
conventions for periodic universes" for Lennard-Jones interactions, and 
"all pairs without cutoff for non-periodic system, Ewald summation for 
periodic systems" for electrostatic interactions.

The code implementing all this is in 
{chimera_install_location}/share/MMMD/MMTKinter.py.

Conrad

On 9/9/2010 7:45 AM, r charbel maroun wrote:
> Dear Chimera users,
>
> What's the value of the dielectric constant used in the Energy minimize
> module ? What's the minimization algorithm used, Steepest descent or
> Conjugate gradients ? Is there any way to modify these values ?
>
> Greetings,
>
> --
> R. Charbel MAROUN, PhD, HDR
> Neurobiologie et Pharmacologie
> Moléculaire
> Centre de Psychiatrie et de
> Neurosciences Broca-Sainte Anne
> (INSERM U894)
> 2ter rue d'Alésia
> 75014 Paris
> FRANCE
> Tél. +33 1 40 78 92 77
> Fax +33 1 45 80 72 93
> e-mail rmaroun at gmail.com <mailto:rmaroun at gmail.com>
> charbel.maroun at inserm.fr <mailto:charbel.maroun at inserm.fr>
>
>
>
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