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

rajat desikan rajatdesikan at gmail.com
Wed May 22 19:40:36 CEST 2013

Hi Mark,
Regarding your statement, how does one check whether g_msd has removed pbc
correctly or not?

On Wed, May 22, 2013 at 10:56 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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