[Openchemistry-developers] Interested in GSoC 2018: Molecular Dynamics

[Marcus D. Hanwell]

On Tue, Feb 20, 2018 at 2:38 PM, Geoffrey Hutchison <
geoff.hutchison at gmail.com> wrote:

> Although I have not worked for any large scale project till date, I would
> love to contribute to some. I am interested in the GSoC, and would like to
> contribute to your code. I am particularly interested in the project
> relating to *Molecular Dynamics *as I found it quite interesting.
>
> Please let me know what other stuff do I need to be familiar with for
> contributing to this project. Also, do let me know about some groundwork
> that I should do before starting this project.
>
>
>
> I'll let Marcus Hanwell comment more. The main goals of the MD project are
> outlined in the wiki - that there are many MD projects (OpenMM, GROMACS,
> Amber, CHARMM, LAMMPS) that all have different file formats (sigh). We'd
> like to add support for visualizing MD calculations, but also handling a
> timeline (e.g., go to frame 105 = 10.5 ps into the simulation), analysis,
> etc.
>
> I am quite open to what you would like to pursue, there is basic support
for loading a trajectory, and stepping through the time steps. That is
really just with XYZ files right now, adding support for LAMMPS, GROMACS,
and OpenMM would be ideal. Looking at how we might generate input to run
the MD codes, and then read the output, and visualize output data.

You would need to get familiar with the capabilities of the codes, and what
important data we are interested in. Reading in energies in time-varying
properties would be very desirable, and a stretch would be looking at how
we might avoid reading the entire trajectory in all at once. We could store
how many time steps there are, other pertinent information, and then load
time step coordinates on demand if that frame is requested.

In general we want to offer better support for MD.

Marcus
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