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

[Mark Abraham]

Along the lines of take a trajectory, and look through it for a frame where
it crosses the periodic boundary of the original cell. Look for artefacts
in the analysis at that time. Or take that frame and use it as a reference
state for whatever trjconv-based PBC-massaging workflow you previously used
before your analysis.

How best to test depends exactly what you're measuring. There are too many
combinations in most GROMACS tools for one test to prove the whole tool
works correctly (or even agrees with how you think it works), so you need
to think about the context that matters to you. You can probably get
creative with editconf's translation options and come up with some fake
trajectories via trjcat that test some edge cases relevant to what you want
to do.

Mark


On Wed, May 22, 2013 at 7:40 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

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