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

[Mark Abraham]

On Wed, May 22, 2013 at 8:05 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> Thanks for the reply,
> trjconv does not have any bugs in removing pbc, right? We can just feed the
> -nojump output to g_msd.
>

Maybe. There are not (yet) any automated tests for the code in these tools.
But probably trjconv -nojump works correctly else we'd have heard more
screaming...

Mark

I am going to output the coordinates and velocities with g_traj and run it
> through my own code :)
>
>
> On Wed, May 22, 2013 at 11:19 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > 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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>
>
> --
> 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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