Added pklplot to the analysis tools
Added excited-state equilibration and md run
Merge branch 'master' of github.com:jhaberstroh/gromacs-scripts
Fixed a grevious error in mdp/fmo/Traj.4.6.mdp, and in associated files computing free energy differences.
Merge branch 'master' of github.com:jhaberstroh/gromacs-scripts into hopper