Normal-mode analysis with vsites or shells works for first molecule of each type only
The routine get_atom_index in mtop_util.cpp works for only one molecule at a time. The routine is used for normal mode analysis with vsites or shells and for analysis of the result using gmx nmeig.
Updated normal modes output for sw-dimer.
Due to a bug in mtop_util.cpp only the first molecule in the
sw-dimer was used in a normal mode analysis. This is fixed in patch
Fixed a bug in gmxtest.pl when comparing two xvg files where the
reference value is zero (it computed the relative difference and
divided by zero). This only showed up in the new output file
Part of #2720
Change get_atom_index to allow multiple molecules.
Make gromacs take into account atoms in all molecules.
This allows Hessian matrix creation to work over all
molecules in a simulation. An update to the regression
tests has been submitted as well.
During fixing of the problem, another problem surfaced in
the normal mode calculations to do with ordering of atoms
which is fixed here as well.