[AMBER] Fast moving system in targeted MD

From: Thomas Exner <thomas.exner.uni-konstanz.de>
Date: Fri, 30 Mar 2012 14:16:18 +0200

Dear Amber users:

During a targeted MD simulation, we saw that our system moves very fast
through the simulation box. This is probably due to the fact, that the
additional forces of the targeting potential do not sum up to zero.
Therefore, there is an additional overall force acting on the solute (in
our case a protein), which accelerates it into one direction. In my
opinion this accelerated system will behave differently than a freely
diffusing system (build up of water waves in front of the solute) and,
therefore, I would like to ask if somebody has ever thought about
removing this additional force and perhaps has already a solution how to
do it.

Thank you very much.

Dr. Thomas E. Exner
Fachbereich Chemie  und Zukunftskolleg
Universitšt Konstanz
78457 Konstanz
Tel.: +49-(0)7531-882015
Fax:  +49-(0)7531-883587
Email: thomas.exner.uni-konstanz.de
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Received on Fri Mar 30 2012 - 05:30:04 PDT
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