Make produced some warnings but gave me h5mdplugin.so and libh5md.so which I've (ln -s) linked to vmd/plugins/LINUXAMD64/molfile/
Trying to load gives:
Info) Dynamically loaded 2 plugins in directory: Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile Info) File loading in progress, please wait. ERROR) Unable to determine file type for file 'binary_mixture.h5'. Assuming pdb. PDB file 'binary_mixture.h5' contains no atoms.