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

[rajat desikan]

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

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
> > > --
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> >
> >
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



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