[gmx-users] Re: MSD normalization

[Mark Abraham]

On 6/12/2011 3:58 AM, Sławomir Stachura wrote:
> 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....

I would be amazed if GROMACS did this. Can you copy and paste from your 
terminal to show this?

Mark

> Hope to have someone join the discussion,
>     Slawomir
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> 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