Subject: Protein dynamics.

From: Laurence Lavelle <lavelle {} mbi.ucla.edu>
Date: Mon, 06 Jun 2005 14:43:50 -0700

In looking at the dynamical motion of a protein, is Amber (Cornell et al. 
(1994) force field) (Amber 99 parameters) considered a reasonably realistic 
protein force field (or, as good as or better than most) ?

In looking at the dynamical motion of a protein (for example using Amber), 
what are the pros and cons to doing Molecular Dynamics vs Langevin Dynamics 
vs Monte Carlo ?

{Some will say it depends on the details (distance dependent dielectric vs 
explicit solvent water molecules, no cutoffs vs with switched or shifted 
cutoffs, with or without periodic boundary conditions, etc.). However I am 
hoping (in addition to the above two questions) to get a general sense of 
how realistic MD, LD and MC are with respect to illustrating protein 
motion. By protein motion I mean a folded protein in a constant temperature 
simulation (for example with a distance dependent dielectric, no 
electrostatic cutoffs, no periodic boundaries) and comparing the protein 
dynamics at different temperatures.
To be explicit, I am not talking about protein folding or unfolding pathways.}

Thanks,
Laurence Lavelle