AMBER Archive (2006)

Subject: Re: AMBER: what is the integration scheme for langevin dynamic used in amber8

From: David A. Case (case_at_scripps.edu)
Date: Sat Apr 01 2006 - 11:18:57 CST

On Sat, Apr 01, 2006, Li Su wrote:
>
> Sorry to bother. I'm curious what is the integration scheme for
> implementing
> langevin dynamics used in amber8. Is there some reference? I checked the
> amber8 manual, although it listed several references for langevin dynamics
> , it didn't point out explicitly it followed a method published in a
> particular reference.

See line 1030 of runmd.f (just search for "Langevin"):

      ! ---simple model for Langevin dynamics, basically taken from
      ! Loncharich, Brooks and Pastor, Biopolymers 32:523-535 (1992),
      ! Eq. 11. (Note that the first term on the rhs of Eq. 11b
      ! should not be there.)

The references listed in the manaul provide background for this choice, which
is really just a minor variant of the BBK algorithm. But the Biopolymers
article was one place where the exact details were written out.

...dac

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