[gmx-users] can we analyse Gromacs trajectory with jupyter?

[Hai Nguyen]

On Fri, Jun 24, 2016 at 7:20 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Not that I know of. From the point of view of someone who already has a
> GROMACS trajectory, the underlying cpptraj tool has support for reading
> .gro and .pdb, but not .xtc or .tng, and you'd also have to decide whether
> you need to produce an equivalent AMBER topology to help analyze your
> particular results. But the idea and the approach look excellent.
>
>
Hi,

cpptraj is able to read TRR format too. cpptraj can read a pdb file as
Topology, so no need to do any conversion to " an equivalent AMBER topology"
I hope that Dan Roe (cc) can find a time slot to implement xtc and  tng
parser soon.

@Albert: meanwhile, you can absolutely use pytraj (python interface of
cpptraj) <https://github.com/Amber-MD/pytraj> and NGLView
<https://github.com/arose/nglview> for your gromacs data analysis and
visualization (need to convert to .trr format thought).

cheers
Hai


> Mark
>
> On Fri, Jun 24, 2016 at 11:27 AM Albert <mailmd2011 at gmail.com> wrote:
>
> > Hello:
> >
> > I recently found that Amber introduced jupyter (http://jupyter.org/) for
> > MD simulation result analysis. One can analyze it through webpage and
> > plot the result nicely with Python and R. One can even display the
> > structure and trajectory in a webpage through WebGL technology. Here are
> > examples:
> >
> >
> http://ambermd.org/tutorials/analysis/tutorial_notebooks/nglview_notebook/
> >
> >
> http://amber-md.github.io/pytraj/latest/tutorials/plot_correlation_matrix.html
> >
> >
> > I am just wondering can we do similar things in Gromacs?
> >
> > Thx a lot
> >
> > Albert
> >
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