Re: AMBER: equilibration with amber5, production of MD with amber7

From: David A. Case <>
Date: Sun, 21 Jan 2007 21:28:46 -0800

On Fri, Jan 19, 2007, Carlos Javier Nuņez Aguero wrote:
> I'am running MDs with amber programs. My system consist of one cyclodextrin,
> one organic molecule and water. I'am doing the equilibration of this system
> without problems using the Amber v5 software.
> Basically, in the equilibration step I increasing the temperature
> (100--->300 K) of the solvent while the complex
> cyclodextrin-organic-molecule remain fixed by means of a force of 500 kcal.
> In the next steps I release the complex (restriction force 500--->0) and run
> 2 ps of production.

> Now, I want re-start the simulation using sander in Amber v7.
> o this combination of equilibration with amber5 & production of MD with
> amber7 is correct?

There *should* be no significant differences between amber5 and amber7, so
in principle this would work. However, if you have really only done 2ps(?)
of "production" run, that represents a very small investment, and I would
think you should start again using a single program. Amber 5 is a very old
program (we are now at version 9), and lots of bugs have been fixed, and
procedures optimized since then.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jan 24 2007 - 06:07:16 PST
Custom Search