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

[Mark Abraham]

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.

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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