Protein dynamics.

[Laurence Lavelle <lavelle {} mbi.ucla.edu>]

 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