AMBER Archive (2004)

Subject: Re: AMBER: langevin dynamics

From: Wei Fu (fuwei_at_adrik.bchs.uh.edu)
Date: Tue Mar 23 2004 - 20:39:44 CST

Dear David,

     Thanks for your explanation, in this case, it is not suitable for our
current study. However, my boss will buy amber8 because we want to run MD
simulation in explicit water model on other system.

Cheers,

Wei

On Tue, 23 Mar 2004, David A. Case wrote:

> 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.
>
> ...regards...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> 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 | http://www.scripps.edu/case
> ==================================================================
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