VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 09 2015 - 16:02:35 CDT

Hi,
  For the time being I've added the H5MD plugin to the VMD molfile
documentation, linked to the H5MD github page you provided.

One thing I noticed is that at present, the H5MD plugin uses ".h5" as
its filename extension, which would match any HDF5-based file, including
those that are incompatible. I would suggest that you consider using
a different default extension (e.g. ".h5md") that is somewhat more unique,
or structure your plugin so that it can be absorbed into a larger plugin
that handles all HDF5-based file formats. This is a similar problem to what
we saw with the AMBER NetCDF formats in the past, where there are also
many other types of data stored in NetCDF files, including alternative ways
of storing molecular data.

I could see another potential way around this in the future by changing
the VMD graphical interface so that it can sort the plugins so that a user's
"favorite" plugin matches a particular file extension in the case that
several plugins are available that all match that file extension.

I'd be curious if users have opinions about that issue.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 09, 2015 at 04:50:37PM -0400, Axel Kohlmeyer wrote:
> On Thu, Apr 9, 2015 at 4:27 PM, Jonas Landsgesell
> <jlandsgesell_at_icp.uni-stuttgart.de> wrote:
> > Sorry the last mail got messed up by my messenger. We have extended the README page on Github, which now lists the purpose and benefits of H5MD along with supporting software. Briefly, H5MD is supposed to be more efficient and user-friendly than the alternatives. The creation of H5MD files is currently supported by LAMMPS, HALMD, and (soon) ESPResSo. It is our hope that other major simulation packages will join. Greetings Jonas Landsgesell
> >
>
> hmmm... i don't know of any H5MD support in LAMMPS, and i look at its
> source code almost any day.
>
> axel.
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/