AMBER Archive (2005)

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

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Wed Jan 05 2005 - 01:29:41 CST

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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