[MMTK] Update Re: NetCDF convention

Jay Billings jayjaybillings at gmail.com
Thu Sep 4 19:57:11 UTC 2008

I found the Snapshot.py example file where you show how to do this. Thanks!

There's a bit of a problem with the output though. I tried opening "
rotation.nc" in nMoldyn and received an error that "This trajectory does not
include time information" and "This is most probably not a trajectory file".
However, there are twenty rotations of the molecule plus its original state
in this file. I tried adding a time variable to the universe with

universe.time = 0
for i in range(20):
     universe.time = i

but this did not work either. Does anyone have any insight into this

On a happier note, I can report that MMTK-2.5.23 and nMoldyn-2.2.5 work on
x86_64 Fedora 9 with numpy. I couldn't get ScientificPython to work with
Numeric and I had to copy the numpy include files to /usr/include/numpy, but
other than that, everything works fine and all tests were successful. :)


On Wed, Aug 13, 2008 at 1:56 PM, Konrad Hinsen <hinsen at cnrs-orleans.fr>wrote:

> On 12.08.2008, at 20:30, Jay Billings wrote:
>  Does anyone know the NetCDF convention used for MMTK trajectory files? I
>> have some data that I want to put into MMTK/NMOLDYN, but I need to know the
>> NetCDF convention. Unfortunately, my data is not in one of the supported
>> formats.
> The netCDF convention is something on my to-do list - which never got
> enough priority to get done, unfortunately.
> By far the easiest way to create MMTK-compatible netCDF files is using MMTK
> itself. The SnapshotGenerator class lets you write almost anything you like
> to a trajectory file from a Python script. The converters that come with
> nMOLDYN use this approach.
> You can also get most of the required information from looking at an
> MMTK-produced netCDF file using ncdump. There are only two required
> variables, "description" and "step", everything else is optional. The format
> for the system definition contained in "description" may not be obvious at
> first, but once you know that it is an executable Python expression, it is
> rather straightforward to analyze. You can also get the description string
> for any MMTK universe using "universe.description()".
> Good luck,
>  Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hinsen at cnrs-orleans.fr
> ---------------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://starship.python.net/pipermail/mmtk/attachments/20080904/08ef2394/attachment.htm>

More information about the mmtk mailing list