AMBER Archive (2005)

Subject: Re: AMBER: Steered Molecular Dynamics with AMBER?

From: David E. Konerding (dekonerding_at_lbl.gov)
Date: Tue Jan 04 2005 - 22:44:15 CST

Rino Ragno wrote:

> Dear Amber's
>
> is any of you out there aware if is it possible to make an SMD
> simulation with amber?
> If yes of how to setup a SMD using amber?
>
> Thank a lot
>
> Rino
>

Rino,

I experimented with adding steering control to AMBER and Chimera (a
molecular visualizer at UCSF) using the Reality Grid steering toolkit.
It was an interesting experiment, and I got as far as being able to
retrieve parameters from a running AMBER simulation and change them (for
exmaple, the TEMP0 variable can be changed, to achieve a dynamic
temperature schedule). In principle, more complex data types like atom
coordinate vectors, etc,
can be modified, but I didn't get that far. The steering toolkit was
architected in a way that made it very difficult to get reliable
behavior. i don't consider my example usable off-the-shelf, but I am
still looking for a good steering toolkit, as I would like to
incorporate this feature into our visual workflow environment.

Dave
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