Re: [AMBER] Steered Molecular Dynamics: Question

From: Dr. Vitaly Chaban <vvchaban.gmail.com>
Date: Thu, 13 Dec 2012 13:20:27 +0100

Hmmm...

Steered MD just means that you "help" your system to evolve in the
desired direction.

What you are speaking about is restraints and is not steered MD in the
common sense. You might apply such restraints to any part of your
system in conventional MD simulations (for example, for more
convenient visualization you will not want your macromolecule to leave
the center of the box), but this trick will NOT make your simulations
steered MD by default.

-- 
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
On Thu, Dec 13, 2012 at 12:35 PM, George Tzotzos <gtzotzos.me.com> wrote:
> The Amber11 manual, in Section 4.5.2, p.108 gives an example of SMD by changing the distance between two atoms. Given that the position of the two atoms are defined by Cartesian coordinates, the push or pull between the two atoms would be directional.
>
> My understanding is (was) that SMD applies spherical restraints and therefore does not specify a certain direction.
>
> Any clarification on the directionality or non-directionality of the SMD method would be greatly appreciated.
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Received on Thu Dec 13 2012 - 04:30:02 PST