Hi,

For particles that diffuse more than half a box length between frames will 
appear as if they haven't moved much, assuming you have periodic boundary 
conditions.

Erik

On 22 May 2013, at 11:41, Anna Akinshina <anna.akinsh...@manchester.ac.uk> 
wrote:

> Dear Gromacs Users,
> 
> I have a question interpreting obtained msd data.
> I need to calculate diffusion coefficient for a single argon atom in a box of 
> water (500 molecules).
> During the calculations (50ns) I write both trr and xtc trajectories, but to 
> save space I write trr for whole system very seldom (every 50000 steps = 100 
> ps)
> but in xtc I have argon only (no water) and write more often (every 1000 
> steps =  2 ps).
> 
> When I analysed the results using g_msd I was surprised that the msd  curves 
> obtained from trr and xtc trajectories differ a lot, what affect the 
> resulting diffusion coefficients.
> 
> If I save trr more often, like every 10000 steps (20ps) the results from both 
>  files coincide.
> 
> Does the msd results depend on how often you write trajectories?
> If yes, what frequency for writing the trajectories for future calculation of 
> the diffusion coefficient would be reasonable and how long should be the 
> calculations?
> 
> Thanks you
> Anna
> -----------------------
> Dr Anna Akinshina
> School of Chemical Engineering & Analytical Science
> The University of Manchester, UK
> 
> 
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