Dear Jason,
Many thanks to you for your detailed descriptions. It really helps!
Thanks again!
Sincerely yours,
Cuiyl
2014-05-27 3:36 GMT+08:00 Jason Swails <jason.swails.gmail.com>:
> On Sun, May 25, 2014 at 10:14 PM, Cuiyl <cuiyinglukitty.gmail.com> wrote:
>
> > Dear Amber Users:
> >
> > I've done some SMD simulations with different starting coordinates
> > taken from equilibrium simulations. I have some questions about
> > the direction of the force. Can we define the direction of the force in
> the
> > SMD simulations? If not, does the method choose the random directions of
> > the forces? How does it choose the directions during the SMD simulation,
> by
> > following the minimum energies in the potential energy surface?
> >
>
> Directionality is determined directly by the reaction coordinate. The
> reaction coordinate is a vector quantity, having both a magnitude and a
> direction (for a distance, for instance, imagine an arrow connecting the
> two points defining that distance). The gradient of the potential of the
> steering energy term is the steering force, whose direction is defined by
> the reaction coordinate itself (the gradient itself is a vector).
>
> If the reaction coordinate is some type of function of particle positions
> (e.g., distances between centers of mass, or the radius of gyration), then
> the forces on the individual atoms are determined using the chain rule
> while differentiating the potential energy expression.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon May 26 2014 - 23:30:02 PDT
