AMBER Archive (2007)

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

From: David A. Case (case_at_scripps.edu)
Date: Sun Jan 21 2007 - 23:28:46 CST

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.

...dac

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