[gmx-users] Conversion of trajectories to netcdf format

Ran Friedman r.friedman at bioc.uzh.ch
Wed Feb 25 09:13:44 CET 2009

I don't know about netcdf, but you can use wordom to convert from xtc to
Contact me off list if you don't succeed - I'm not sure whether the
online documentation of wordom is up-to-date.


Tobias Unruh wrote:
> Hi,
> I would like to use nMolDyn for the analysis of the GROMACS trajectories.
> I tried VMD and catdcd to convert trr/tpr files to dcd/pdb files. But the
> conversion of the dcd/pdb files to nc (netcdf) files using the dcd_to_nc
> program of the nMolDyn package does not work. Obviously the header of the
> dcd file differs from what is expected by the dcd_to_nc program which
> uses
> Does anyone know how to convert the GROMACS trajectories such that
> nMolDyn can be used for calculation of correlation and intermediate
> scattering functions?
> I appreciate any suggestion.
> Regards Tobias
> -- 
> Tobias Unruh
> TU Muenchen, FRM-II
> 85747 Garching, Germany
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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