├── README.md ├── docs └── python-libs.tex ├── examples ├── CGenFF │ ├── N-methylacetamide │ │ ├── LIG_ffbonded.itp │ │ ├── after_cg.g96 │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── output │ │ ├── topol.top │ │ └── traj.trr │ ├── charmm36.ff │ │ ├── atomtypes.atp │ │ ├── bugs │ │ ├── cmap.itp │ │ ├── ffbonded.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── gb.itp │ │ ├── hack.itp │ │ ├── ions.itp │ │ ├── merged.arn │ │ ├── merged.c.tdb │ │ ├── merged.hdb │ │ ├── merged.n.tdb │ │ ├── merged.r2b │ │ ├── merged.rtp │ │ ├── merged.vsd │ │ ├── mol │ │ │ ├── aald.itp │ │ │ ├── aald.pdb │ │ │ ├── acet.itp │ │ │ ├── acet.pdb │ │ │ ├── acey.itp │ │ │ ├── acey.pdb │ │ │ ├── acox.itp │ │ │ ├── acox.pdb │ │ │ ├── anil.itp │ │ │ ├── anil.pdb │ │ │ ├── benx.itp │ │ │ ├── benx.pdb │ │ │ ├── benz.itp │ │ │ ├── benz.pdb │ │ │ ├── brob.itp │ │ │ ├── brob.pdb │ │ │ ├── chlb.itp │ │ │ ├── chlb.pdb │ │ │ ├── flub.itp │ │ │ ├── flub.pdb │ │ │ ├── form.itp │ │ │ ├── form.pdb │ │ │ ├── forx.itp │ │ │ ├── forx.pdb │ │ │ ├── imia.itp │ │ │ ├── imia.pdb │ │ │ ├── iodb.itp │ │ │ ├── iodb.pdb │ │ │ ├── mamm.itp │ │ │ ├── mamm.pdb │ │ │ ├── mamx.itp │ │ │ ├── mamx.pdb │ │ │ ├── mamy.itp │ │ │ ├── mamy.pdb │ │ │ ├── meoh.itp │ │ │ ├── meoh.pdb │ │ │ ├── meox.itp │ │ │ ├── meox.pdb │ │ │ ├── mqtr │ │ │ │ ├── benz.mqtr │ │ │ │ ├── chlb.mqtr │ │ │ │ └── tolu.mqtr │ │ │ ├── phen.itp │ │ │ ├── phen.pdb │ │ │ ├── prox.itp │ │ │ ├── prox.pdb │ │ │ ├── prpa.itp │ │ │ ├── prpa.pdb │ │ │ ├── prpx.itp │ │ │ ├── prpx.pdb │ │ │ ├── pyr1.itp │ │ │ ├── pyr1.pdb │ │ │ ├── sol.pdb │ │ │ ├── tolu.itp │ │ │ └── tolu.pdb │ │ ├── nbfix.itp │ │ ├── silcs.itp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip4p.itp │ │ └── watermodels.dat │ └── quinoline │ │ ├── LIG_ffbonded.itp │ │ ├── after_cg.g96 │ │ ├── cg.tpr │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── md.log │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── quinoline-g4.log.gz │ │ ├── spectrum.xvg │ │ ├── topol.top │ │ └── traj.trr ├── GAFF-ESP │ ├── N-methylacetamide │ │ ├── N-methylacetamide-3-oep.log.gz │ │ ├── after_cg.g96 │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── topol.top │ │ └── traj.trr │ ├── carbon-monoxide │ │ ├── after_cg.g96 │ │ ├── carbon-monoxide-3-oep.log.gz │ │ ├── carbon-monoxide-g4.log.gz │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── spectrum.xvg │ │ ├── topol.top │ │ └── traj.trr │ └── quinoline │ │ ├── after_cg.g96 │ │ ├── conf.gro │ │ ├── eigenfreq.xvg │ │ ├── eigenval.xvg │ │ ├── eigenvec.trr │ │ ├── ener.edr │ │ ├── mdout.mdp │ │ ├── minimize.log │ │ ├── minimize.tpr │ │ ├── nm.log │ │ ├── nm.mtx │ │ ├── nm.tpr │ │ ├── old.top │ │ ├── quinoline-g4.log.gz │ │ ├── spectrum.xvg │ │ ├── topol.top │ │ └── traj.trr └── MDP │ ├── cg.mdp │ └── nm.mdp ├── refs └── alfred_refs.bib └── scripts ├── CalculateSpectrum ├── mk_spectrum.py ├── spectrum_classes.py └── spectrum_functions.py ├── GenerateSpectra ├── get_exp_data.py ├── get_exp_data.sh ├── mixing_spectra.py ├── mk_spectra.py ├── run_spectrum.sh ├── spectrum_classes.py ├── spectrum_functions.py └── spectrum_functions.pyc ├── calculate_intensity_from_charge_theory_and_example.ipynb ├── charge_instead_of_dipole_moment.ipynb ├── mk_spectrum.py ├── remove_nan.py ├── run_nm.py └── visualization_of_spectra.ipynb /README.md: 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