Re: AMBER: langevin dynamics

From: David A. Case <>
Date: Tue, 23 Mar 2004 14:33:01 -0800

On Sun, Mar 21, 2004, Wei Fu wrote:
> We want to do Langevin Dynamics simulation in vacuum on a large protein
> (around 1000 residues).

It is possible to do this in Amber 8. I am reluctant to recommend this
to anyone, however for two reasons:

a. The properties of proteins using a "vacuum" force field are generally not
    very good. A major goal of implicit solvent models is to allow one to
    do "vacuum-like" simulations with a more realistic account of the
    conformational energetics involved.

b. The code is not optimized for efficiency for this sort of calculation.
    Since it seems that your primary purpose is so save time, Amber might
    not be a good option for you.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Tue Mar 23 2004 - 22:53:00 PST
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