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@gmail.com charbel.maroun@inserm.fr
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@gmail.com <mailto:rmaroun@gmail.com> charbel.maroun@inserm.fr <mailto:charbel.maroun@inserm.fr>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Conrad Huang -
r charbel maroun