Re: AMBER: Steered Molecular Dynamics with AMBER?

From: aldo jongejan <>
Date: Wed, 05 Jan 2005 08:46:44 +0100


Maybe just a little off-topic, but related to steered molecular
dynamics in a way. Some people at the Technical University of
Delft (The Netherlands), mainly Michal Koutek, have been integrating
Molecular dynamics with virtual reality. A ligand could be steered
on-the-fly out of a pocket using GROMACS, just by exerting a force on
the atoms. If I remember correctly, it resembles studies performed
in the group of Klaus Schulten (I remember having seen some people
dragging molecules through a ion-channel with a VR-glove). Koutek
and coworkers have been able to bring this into the from of a
simple Workbench. I have included some reference to this work and
a spin-off company (FolDyne). I see no reason why this couldn't be
done with AMBER...





Piotr Cieplak wrote:

> Hi
> Speaking of SMD in AMBER we just got accepted a paper about application
> of the SMD method in Amber to some simple cases:
> Application of the Steered Molecular Dynamics (SMD) to study
> DNA--drug complexes and probing helical propensity of amino acids.
> M.Orzechowski, P.Cieplak
> accepted, J.Phys. Condens.Matter, 2004
> Since the SMD method is not implemented yet in the code, we
> use an external script that modifies restart MD files to pull
> molecule along a predefined line.
> For pulling we use an artificial atom approach.
> We plan to implement the method into the code without the need
> of using external scripts.
> Piotr
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Aldo Jongejan
Molecular Design
LACDR/Dept. Medicinal Chemistry		
Vrije Universiteit Amsterdam		
De Boelelaan 1083		e-mail:
1081 HV Amsterdam		tlf: +31 (0)20 5987612
The Netherlands			fax: +31 (0)20 5987610
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Received on Wed Jan 05 2005 - 08:53:00 PST
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