[gmx-users] Re: MSD normalization

[Sławomir Stachura]

Hi,

There is something interesting concerning these MSD calculations. If I treat Centre of Mass MSD  if it'd be expressed not in nm^2/ps , but Angstroms^2/ps, I get ideally the same results as for mass-weighted ones. And it's true for all my three cases, in which I performed simulation of different times. Is that possible there is some bug in MSD? Because as for me it looks so....
Hope to have someone join the discussion,
   Slawomir





Wiadomość napisana przez Sławomir Stachura w dniu 2011-12-04, o godz. 22:38:

> 
> Hi,
> 
> I was just wondering how MSDs in Gromacs are normalized. I am calculatiing MSDs for my lipid system of different timesteps of simulation and I get much higher results for centre of mass calculations in comparison to mass-weighted one.  And I thought about normalization issue, but I couldn't find any informations concerning that topic in manual.
> I'd be grateful if someone could explain how mean square displacement is normalized.
> 
> Cheers,  
>   Slawomir