[MMTK] NetCDF convention

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed Aug 13 17:56:14 UTC 2008

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  

Good luck,
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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