[gmx-users] BD and SD equations
Mark.Abraham at anu.edu.au
Fri Jul 8 18:17:37 CEST 2011
On 9/07/2011 1:36 AM, Marcelo A. Carignano wrote:
> Hi all,
> Stochastic dynamics is described in section 3.8 of the Manual (v. 4.5)
> Equation 3.108 is dimensionally incorrect, or at least I cannot
> understand it.
> Left hand side is a force,
Specifically, mass * length * time^-2. Note that (d^2 r)/(d t^2) is
(d/dt) (d/dt) r, which makes the dimensionality more clear.
> and the first term on the right hand side has a missing length in the
> numerator to be a force.
It has a missing length dimension to be an *energy* :-)
> This is according to the definition of xi, right below the equation,
> as having units of 1/ps.
> Brownian dynamics, described in section 3.9, also has a problem
> (again, in my opinion)
> gamma is defined as mass/xi, but it is using gamma=mass*xi that we can
> recover the two terms of the SD case
> (still with the wrong dimensions)
Seems OK to me, similarly.
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