Subject: Re: CCL:damped molecular dynamics

From: Richard Gillilan <[email-masked]>
Date: Wed, 30 Oct 2002 09:10:10 -0500

In dynamics with friction and stochastic terms there is the 
tendency to mask problems in the underlying trajectory 
integration/dynamics. I believe the step size should be 
chosen so that zero-friction dynamics is stable for long
time ... that way you know the underlying dynamics is good.
Usually for dynamics, you would choose a stepsize of 1 or 2
fsec when hydrogen atoms are present. With a unified atom model
or bond-length constraints you can go larger. The step size you
need must be smaller than a typical oscillation period for any 
coordinate. Oscillation period depends upon both the stiffness
of the spring and the effective mass of the atom or body.

You could then turn up the friction a little to give you
what you want. I assume you are using it as a sort of
simulated annealing?

I would love to know how others choose good friction terms for 
Langevin type simulations. Perhaps others will comment.

 Richard Gillilan 
 MacCHESS, Cornell

> 2) What are good strategies to decide the friction coefficient and time
> step? I noticed that if the time step is too large, the kinetic
> instabilities are common.
> 
> thanks for any help.
> 
> Aaron Deskins
> Purdue University
>

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From: Rick Venable <[email-masked]>
Date: Wed, 30 Oct 2002 17:47:22 -0500

First, a citation--

---------------
LONCHARICH RJ, BROOKS BR, PASTOR RW
LANGEVIN DYNAMICS OF PEPTIDES - THE FRICTIONAL DEPENDENCE OF
ISOMERIZATION RATES OF N-ACETYLALANYL-N'-METHYLAMIDE
BIOPOLYMERS 32 (5): 523-535 MAY 1992 

Abstract:

The rate constant for the transition between the equatorial and axial
conformations of N-acetylalanyl-N'-methylamide has been determined from
Langevin dynamics (LD) simulations with no explicit solvent. The
isomerization rate is maximum at collision frequency gamma = 2 ps-1,
shows diffusive character for gamma greater-than-or-equal-to 10 ps-1,
but does not approach zero even at gamma = 0.01 ps-1. This behavior
differs from that found for a one-dimensional bistable potential and
indicates that both collisional energy transfer with solvent and
vibrational energy transfer between internal modes are important in the
dynamics of barrier crossing for this system. It is suggested that
conformational searches of peptides be carried out using LD with a
collision frequency that maximizes the isomerization rate (i.e., gamma
almost-equal-to 2 ps-1). This method is expected to be more efficient
than either molecular dynamics in vacuo (which corresponds to LD with
gamma = 0) or molecular dynamics in solvent (where dynamics is largely
diffusive).
---------------

	In essence, low friction (gamma = 2 ps-1) can accelerate barrier
crossing rates, and improve sampling of phase space.  For a simulated
annealing or other sampling strategy, where you are not interested in
timescales of motions, I highly recommend using low friction.  For
reference, the collision frequency of water is ca. 50 ps-1.

> Langevin type simulations. Perhaps others will comment.

-------------------
> > instabilities are common.

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Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   [email-masked]
ALT email:  [email-masked]
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