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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
http://coffee.sdsc.edu/rcw/plane_vids/
http://www.rosswalker.co.uk/movie_sounds/
Received on Sun Apr 02 2006 - 06:10:18 PDT
