[MMTK] NetCDF convention

Jay Billings jayjaybillings at gmail.com
Wed Aug 13 18:27:06 UTC 2008


Konrad,

Thanks very much for your response. I'll give the SnapshotGenerator a try.

I'm attempting to write a converter for Materials Studio's Forcite
trajectory files, which are stored in simple XML, to the MMTK-netcdf format.
If I get it working, I will make sure to send it to you.

Jay

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
> ---------------------------------------------------------------------
>
>
>
>
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