[gmx-users] Re: MSD and frequency of writing trajectories

[Mark Abraham]

On Wed, May 22, 2013 at 4:49 PM, Yutian Yang <yyang18 at syr.edu> wrote:

> Erik,
>
> Do you mean that if the particle diffuses too fast, it will appear like it
> doesn't move because of the PBC?
>

Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect

I have another issue. If I have a polymer chain with the length almost the
> same as the box length. It is possible that the COM diffusion of the chain
> may appear it does not move or move backward due to PBC, right?
>

Depends how you've post-processed your trajectory and/or the GROMACS tool
treats PBC. There have been bugs in the latter. Nobody's issued any
warranties, so everyone should certainly be checking a) that the tool works
they way they think it does, and b) that the tool gives the right answer on
a relevant test case. Or the world may end when some reviewer points out an
analysis artefact some dark day...

Mark