AMBER Archive (2007)

Subject: Re: AMBER: Confusion about Langevin dymamics

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Aug 31 2007 - 08:52:02 CDT

Langevin dynamics is usually used with implicit solvent.
Even then there are issues; for example, real solvent viscosity
depends on solvent exposure and is anisotropic, while neither
is taken into account in Amber's implementation.
If used with explicit solvent, it is a good idea to use low viscosity for
the reasons that you state.

On 8/31/07, Hayden Eastwood <s0237717_at_sms.ed.ac.uk> wrote:
>
> Dear AMBER users
>
> I have puzzled for some time about the Langevin equation and I wonder if
> anyone can answer this question for me:
>
> Why does the Langevin equation possess a frictional coefficient?
>
> I am simulating a protein in explicit solvent and it seems to me that the
> explicit water particles already give rise to a "frictional" term. Thus,
> it
> appears that there are 2 origins of friction when employing Langevin
> dynamics; that of the actual bulk water, and that of the imaginery bulk
> water (ie that which is implicit to the langevin equation). Surely, this
> "double counting" of friction just slows phase space sampling and is
> otherwise needless? Furthermore, does this not adversely affect comparison
> with some experiments, since the "double" friction term inevitably means
> that phase space sampling is "slower" than the experimental reality. Ie.
> How
> can you be certain of molecular time scale events if the bulk water being
> modelled over-estimates the viscosity of the surrounding medium?
>
> Many thanks
>
> Hayden Eastwood
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu