Subject: RE: MD Constraints

From: [email-masked] (Thomas M. O'Connell)
Date: Wed, 19 Oct 94 05:59:56 -0700

Dear Edgardo,

Regarding your question about extending the conformational
sampling of a MD run using parameter rather than algorithmic
changes I would like to point out the following references.

1) Mass and Step Lenght Optimization for the Calculation
of Equilibrium Properties by MD Simulations
R. Pomes and J. A. McCammon, Chem. Phys. Lett 166(4) 425 1990

This paper discusses the merits of globally increasing the mass
of the atoms so that a longer timestep ( several fs ) can be
used, therefore facilitating longer simulations. The authors found
that the rate of conformational sampling was somewhat reduced with
the increased mass, but the longer dyanmics offsets this somewhat.
This method is best used for calculating equilbrium thermodyamic
properites, but it may be of use to you.

2) Virtual Rigid Body Dynamics
T. Head-Gordon and C. L. Brooks, Biopolymers 31, 77-100, 1991
This paper is probably of more direct relevance to you.  It
describes a method for reduction of the full atomic representation
followed by selectively constraining the system.  This method
is available in XPLOR 3.0 and is described in the manual.

Good Luck,
                Tom O'C.

*******************************************************
  Thomas M. O'Connell Ph.D.                               
  Laboratory of Molecular Biophysics                    
  National Institute of Environmental Health Sciences 
  [email-masked]	 ph  919-541-3872      
                                 fax        -7880