On Tue, Jan 26, 2016 at 10:27 AM, Lara rajam <lara.4884.gmail.com> wrote:
> Dear Amber !
>
> Thank you for the reply. I am not interested in steered dynamics , rather I
> want to do a kind of targeted dynamics ,
> So that I can bring the ligand to the receptor binding site from a far
> distance. I have gone through the literatures ,
> but I have problem in handling forces to make the decrease in distance as
> linear component of time,
>
You say you don't want to do steered molecular dynamics, but what you
describe wanting to do IS steered molecular dynamics.
What you describe is a non-equilibrium, biased simulation. Steered MD is
implemented by moving the center of a harmonic restraint potential along a
reaction coordinate linearly as the simulation progresses.
How is this not what you want to do?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 26 2016 - 08:00:07 PST
