[gmx-users] BD and SD equations

[Mark Abraham]

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.

Mark