[gmx-users] MSD and frequency of writing trajectories

Erik Marklund erikm at xray.bmc.uu.se
Wed May 22 13:17:41 CEST 2013


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.


On 22 May 2013, at 11:41, Anna Akinshina <anna.akinshina at 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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