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 - 13:00:02 PDT
