convert namd structure/coordinate files to gromacs topology file

From: Glenn Johnson (
Date: Fri Mar 18 2005 - 14:00:54 CST

I am using NAMD for MD simulations and I wanted to try to use some of
the Gromacs analysis tools. I have converted the trajectory file from
dcd to trr with VMD but the gromacs analysis tools need a tpr file as
well. How can I produce one?

There are apparently two cases of tpr files, a run control file and a
Structure+Mass(db) file. The latter can be a pdb format file but none
of the pdb files I have produced with psfgen have the masses in them.
Does anyone know where the mass goes in this case?


Glenn Johnson <>
U. S. Department of Agriculture

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