[gmx-users] MSD and frequency of writing trajectories

Mark Abraham mark.j.abraham at gmail.com
Wed May 22 13:19:50 CEST 2013

Sure. What's the MSD of a pendulum if you only sample at a rate equal to
the period? How often you want to sample depends on the time scale of what
you want to observe. That might be up to you to measure :-)


On Wed, May 22, 2013 at 11:41 AM, 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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