updated DREIDING to fix hydrogen bonds
The order of the @atom types listed in the "dreiding.lt" file has been modified to (hopefully) make sure that LAMMPS does not get confused regarding which atoms are hydrogen-bond donors and acceptors. This is an attempt to address issue #46.
I think this is working now. However, if you use hydrogen bonds with DREIDING, then please double-check the "system.in.settings" files created by moltemplate.sh, and check each "pair_coeff" command containing the text "hbond/dreiding/lj". Make sure that the atom types are listed in the correct order, with donor atom types listed before acceptor atoms. Before doing this, I suggest running cleanup_moltemplate.sh first. (Otherwise the number of pair_coeff commands in the "system.in.settings" file might be too large to check by hand. The "cleanup_moltemplate.sh" program should work without issue with DREIDING simulation files as long as your main LT file is named "system.lt". Just type "cleanup_moltemplate.sh" into the terminal after running moltemplate.sh. In the future, when "dreiding.lt" is debugged, this extra effort won't be necessary.)
Many thanks to Aileen Huang (ahuang5@student.gn.k12.ny.us) for reporting this issue!