Re: AMBER: Steered Molecular Dynamics with AMBER?

From: Adrian E. Roitberg <roitberg.qtp.ufl.edu>
Date: Wed, 05 Jan 2005 09:13:10 -0500

Dear Piotr,
Could you send me a pdf file with your paer on SMD ?
Thanks !!!

Cheers
adrian


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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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Wed Jan 05 2005 - 14:53:00 PST