AMBER: equilibration with amber5, production of MD with amber7

From: Carlos Javier Nuņez Aguero <>
Date: Fri, 19 Jan 2007 14:47:05 -0600

Hi all,

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. (I have
access to amber7
mounted in one cluster and is very difficult to me see the graphic
environment of t-leap).

My question is:

o this combination of equilibration with amber5 & production of MD with
amber7 is correct?
o what do you think about this?

Thanks & Regards,
Carlos Javier
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Received on Sun Jan 21 2007 - 06:07:41 PST
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