See the Wikipedia article about Langevin dynamics:
http://en.wikipedia.org/wiki/Langevin_dynamics -- specifically the first
equation (not the second two describing the requirements that the random
numbers be uncorrelated). The first term is "ma" in Newton's equations
F=ma. Note that the first term on the RHS of the equation is the negative
gradient of the potential, or Force. Therefore, neglecting the second two
terms on the RHS, you have exactly Newton's equations (for Newtonian
dynamics). The second term is a frictional term (i.e., the faster
something goes, the stronger the frictional force on it). Notice that the
velocity is a vector, and so the frictional term always opposes the
direction of travel. The last term on the RHS is a 'random kick'.
It is this last part that is temperature-dependent term that is responsible
for temperature regulation.
HTH,
Jason
On Mon, Jul 16, 2012 at 6:55 PM, Qian Wang <qwang.mail.uh.edu> wrote:
> Hi,
>
> I just wonder how the Langevin Dynamics (LD) works in Amber. When we set
> gamma_ln > 0, do we use LD exclusively? Do we invoke Newtonian dynamics in
> this case?
> Could you please explain how is this related to temperature regulation?
> Can we run Newtonian dynamics with Langevin thermostat?
>
> Sincerely,
> Qian
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 16 2012 - 18:30:02 PDT
