Re: AMBER: langevin dynamic in sander

From: David A. Case <case.scripps.edu>
Date: Tue, 23 Nov 2004 08:21:30 -0800

On Tue, Nov 23, 2004, Stefano.Pieraccini.unimi.it wrote:

> I wonder if in langevin dynamics in sander the
> random force to simulate the interaction of the
> solute with the solvent molecules are applied to
> all the atoms of the solute or in some way only to
> the surface atoms, to simulate the specific
> feathure of an interaction of (for example) water
> molecules hitting directly the surface and not the
> interior of a protein.

The random force affects all atoms of the molecule.

.....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Nov 23 2004 - 16:53:00 PST
Custom Search