├── README.md ├── doc └── BOCS_user_manual.pdf ├── force-matching ├── CMakeLists.txt ├── LICENSE ├── README ├── scripts │ ├── translate_table.py │ ├── translate_top.py │ └── translate_top_fn.py └── src │ ├── CMakeLists.txt │ ├── calc_grids.c │ ├── calc_grids.h │ ├── calc_ref_potential.c │ ├── calc_ref_potential.h │ ├── cgff.c │ ├── cgff.c~ │ ├── cgff_fn.c │ ├── cgff_fn.h │ ├── cgff_types.h │ ├── cgmap.c │ ├── cgmap_legacy.c │ ├── gromacs_topology.c │ ├── gromacs_topology.h │ ├── io_output.c │ ├── io_output.h │ ├── io_read.c │ ├── io_read.h │ ├── read_map.c │ ├── read_map.h │ ├── read_parameters.c │ ├── read_parameters.h │ ├── safe_mem.c │ ├── safe_mem.h │ ├── solv_lin_eqns.c │ ├── solv_lin_eqns.h │ ├── table_functions.c │ ├── table_functions.h │ ├── table_types.h │ ├── tables.c │ ├── transf_map.c │ ├── transf_map.h │ ├── translator.c │ ├── wnoid_math.c │ └── wnoid_math.h ├── pressure-matching ├── CMakeLists.txt ├── LICENSE ├── README └── src │ ├── CMakeLists.txt │ ├── basis.c │ ├── basis.h │ ├── distro.c │ ├── distro.h │ ├── io.c │ ├── io.h │ ├── plot_basis.c │ ├── pressure_matching.c │ ├── pressure_matching_fn.c │ ├── pressure_matching_fn.h │ ├── pressure_matching_types.h │ ├── safe_mem.c │ ├── safe_mem.h │ ├── solv_lin_eqns.c │ └── solv_lin_eqns.h └── tutorials ├── 1-site_methanol ├── aa_simulation │ ├── methanol.4.5.3.mdp │ ├── methanol.5.1.4.mdp │ ├── methanol.gro │ ├── methanol.top │ └── methanol_oplsaa.itp ├── cg_sim │ ├── cg_methanol.4.5.3.mdp │ ├── cg_methanol.5.1.4.mdp │ ├── cg_methanol.gro │ ├── cg_methanol.ndx │ └── cg_methanol.top └── coarse_graining │ ├── cg_methanol.4.5.3.mdp │ ├── cg_methanol.5.1.4.mdp │ ├── cg_methanol.gro │ ├── cg_methanol.ndx │ ├── cg_methanol.top │ ├── inp.txt │ ├── map.methanol.top │ ├── par.txt │ └── results │ ├── L.Pair_Interaction.total.MEOMEO.dat │ ├── b_forces.Pair_Interaction.total.MEOMEO.dat │ ├── b_struct.Pair_Interaction.total.MEOMEO.dat │ ├── f_forces.Pair_Interaction.total.MEOMEO.dat │ ├── f_struct.Pair_Interaction.total.MEOMEO.dat │ ├── g.Pair_Interaction.total.MEOMEO.dat │ ├── g_cnt.Pair_Interaction.total.MEOMEO.dat │ ├── save.FF.dat │ ├── save.L.dat │ ├── save.M.dat │ ├── save.M2.dat │ ├── save.Nf.dat │ ├── save.b_forces.dat │ ├── save.b_struct.dat │ ├── save.d2M.dat │ ├── save.d2b.dat │ ├── save.g.dat │ ├── save.g_cnt.dat │ └── save.rescale.dat ├── heptol_xn ├── aa_simulations │ ├── 1_1_heptol │ │ ├── 1_1_HEP_TOL.gro │ │ ├── 1_1_HEP_TOL.mdp │ │ ├── 1_1_HEP_TOL.top │ │ ├── heptane.itp │ │ └── toluene.itp │ ├── 1_4_heptol │ │ ├── 1_4_HEP_TOL.gro │ │ ├── 1_4_HEP_TOL.mdp │ │ ├── 1_4_HEP_TOL.top │ │ ├── heptane.itp │ │ └── toluene.itp │ ├── 2_3_heptol │ │ ├── 2_3_HEP_TOL.gro │ │ ├── 2_3_HEP_TOL.mdp │ │ ├── 2_3_HEP_TOL.top │ │ ├── heptane.itp │ │ └── toluene.itp │ ├── 3_2_heptol │ │ ├── 3_2_HEP_TOL.gro │ │ ├── 3_2_HEP_TOL.mdp │ │ ├── 3_2_HEP_TOL.top │ │ ├── heptane.itp │ │ └── toluene.itp │ └── 4_1_heptol │ │ ├── 4_1_HEP_TOL.gro │ │ ├── 4_1_HEP_TOL.mdp │ │ ├── 4_1_HEP_TOL.top │ │ ├── heptane.itp │ │ └── toluene.itp ├── coarse_graining │ ├── 1_1_heptol │ │ ├── cg.1_1_HEP_TOL.gro │ │ ├── cg.1_1_HEP_TOL.mdp │ │ ├── cg.1_1_HEP_TOL.ndx │ │ ├── cg.1_1_HEP_TOL.top │ │ ├── inp.txt │ │ ├── map.1_1_HEP_TOL.top │ │ └── par.txt │ ├── 1_4_heptol │ │ ├── cg.1_4_HEP_TOL.gro │ │ ├── cg.1_4_HEP_TOL.mdp │ │ ├── cg.1_4_HEP_TOL.ndx │ │ ├── cg.1_4_HEP_TOL.top │ │ ├── inp.txt │ │ ├── map.1_4_HEP_TOL.top │ │ └── par.txt │ ├── 2_3_heptol │ │ ├── cg.2_3_HEP_TOL.gro │ │ ├── cg.2_3_HEP_TOL.mdp │ │ ├── cg.2_3_HEP_TOL.ndx │ │ ├── cg.2_3_HEP_TOL.top │ │ ├── inp.txt │ │ ├── map.2_3_HEP_TOL.top │ │ └── par.txt │ ├── 3_2_heptol │ │ ├── cg.3_2_HEP_TOL.gro │ │ ├── cg.3_2_HEP_TOL.mdp │ │ ├── cg.3_2_HEP_TOL.ndx │ │ ├── cg.3_2_HEP_TOL.top │ │ ├── inp.txt │ │ ├── map.3_2_HEP_TOL.top │ │ └── par.txt │ ├── 4_1_heptol │ │ ├── cg.4_1_HEP_TOL.gro │ │ ├── cg.4_1_HEP_TOL.mdp │ │ ├── cg.4_1_HEP_TOL.ndx │ │ ├── cg.4_1_HEP_TOL.top │ │ ├── inp.txt │ │ ├── map.4_1_HEP_TOL.top │ │ └── par.txt │ └── extended_ensemble │ │ ├── inp.txt │ │ ├── lammps_tables.sh │ │ ├── make_gmx_table.sh │ │ └── par.txt └── pressure_matching │ ├── iteration_one │ ├── config.ini │ └── test_sim │ │ ├── cgheptol.lmp │ │ └── data.cgheptol │ ├── iteration_zero │ ├── config.ini │ └── test_sim │ │ ├── cgheptol.lmp │ │ └── data.cgheptol │ └── rerun │ ├── cg.rerun.1_1_HEP_TOL.gro │ ├── cg.rerun.1_1_HEP_TOL.mdp │ ├── cg.rerun.1_1_HEP_TOL.ndx │ └── cg.rerun.1_1_HEP_TOL.top └── lj_recovery ├── LJ.gro ├── LJ.mdp ├── LJ.top ├── inp.txt ├── par.txt └── results ├── L.Pair_Interaction.total.LJLJ.dat ├── b_forces.Pair_Interaction.total.LJLJ.dat ├── b_struct.Pair_Interaction.total.LJLJ.dat ├── f_forces.Pair_Interaction.total.LJLJ.dat ├── f_struct.Pair_Interaction.total.LJLJ.dat ├── g.Pair_Interaction.total.LJLJ.dat ├── g_cnt.Pair_Interaction.total.LJLJ.dat ├── out.total.txt ├── save.FF.dat ├── save.L.dat ├── save.M.dat ├── save.M2.dat ├── save.Nf.dat ├── save.b_forces.dat ├── save.b_struct.dat ├── save.d2M.dat ├── 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