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
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
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