[gmx-users] BD and SD equations

Marcelo A. Carignano cari at northwestern.edu
Fri Jul 8 19:20:39 CEST 2011

Thank you Mark.

On Jul 8, 2011, at 11:17 AM, Mark Abraham wrote:

> 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* :-)

you are of course right, I should not work in the mornings!

>> 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.

But what is gamma?  mass*xi (still is before noon over here)
If so, the manual has a missprint.

> Mark
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