AMBER Archive (2004)

Subject: Re: AMBER: langevin dynamic in sander

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 23 2004 - 10:21:30 CST

On Tue, Nov 23, 2004, Stefano.Pieraccini_at_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

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