AMBER: multi chain simulations

From: priya priya <>
Date: Thu, 4 Oct 2007 11:30:27 +0100 (BST)

 Dear All,

I am trying to run MD using multi chain system in implicit solvent by setting up a box using setBox command in leap, but generalized born simulations can only be run for non-periodic systems, so the chains are diffusing away from each other during the simulation run.
I want to create an imginary sphere around the molecule and if the distance of atom from the center of mass is longer than the length of the imaginary sphere, then, i want to apply additional force imposed on that atom (the direction is to the center of mass).
What options can I use to keep the chains in a box (not flying far away from each other) whose sphere I am specifying.
Any suggestions how to do it in amber9


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Received on Sun Oct 07 2007 - 06:07:24 PDT
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