AMBER Archive (2006)

Subject: Re: AMBER: freeze interval vibrations

From: David A. Case (
Date: Wed May 24 2006 - 14:00:35 CDT

On Wed, May 24, 2006, Eric Hu wrote:

> Hi, I am conducting a virus assembly simulation. I want to freeze the
> subunit interval vibration (saving time) during md since I am more
> interested in the assembly process. Does amber have any functional to
> accomplish this? Thanks.

Amber does not really support the notion of "rigid bodies" in dynamics.
For something small, you could force rigidity by introducing lots of
constraints, but that would not be feasible for something the size of a virus.

Basically, if you want to simulate virus assembly with Amber, you will
probably need to construct a lower resolution model. This is possible, but
quite cumbersome: Amber is really designed for atomic level simulations.


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