├── .DS_Store ├── LICENSE ├── README.md ├── docs └── user_guide │ ├── 1.DataPreparation.md │ ├── 2.LongRangeParameters.md │ ├── 3.ShortRangeParameters │ └── 4.GNNBondingInteraction ├── example ├── 0_modify_admp_to_mpid.py ├── 1_map_mpid_atype_to_opls.py ├── 1_merge_bond_to_mpid.py ├── 2_map_opls_atype_to_mpid.py ├── EC.pdb ├── EC.xml ├── caff_5_mpid_slater_bond.bk.xml ├── caff_5_mpid_slater_bond.xml ├── example_Li_PF6_DMC-EC │ ├── __pycache__ │ │ ├── driver.cpython-39.pyc │ │ ├── eann.cpython-39.pyc │ │ ├── eapnn.cpython-39.pyc │ │ ├── gnn.cpython-39.pyc │ │ ├── graph.cpython-39.pyc │ │ └── pairwisenn.cpython-39.pyc │ ├── clear.sh │ ├── client_dmff.py │ ├── driver.py │ ├── eapnn.py │ ├── err │ ├── gen_md_pdb.py │ ├── init.pdb │ ├── init_extracted.pdb │ ├── init_init.pdb │ ├── init_remaining.pdb │ ├── input.xml │ ├── log │ ├── log_dmff │ ├── logfile │ ├── model.pdb │ ├── out │ ├── params_ml.pickle │ ├── params_sgnn.pickle │ ├── params_sgnn_ABn.pickle │ ├── pdb_bank │ │ ├── BF4.pdb │ │ ├── DFP.pdb │ │ └── PF6.pdb │ ├── phyneo_ecl.xml │ ├── run_client_dmff.sh │ ├── run_server.sh │ └── sub.sh ├── gnn_torch_revision.py ├── graph_torch_revision.py ├── jax2torch.py ├── modify_xml │ ├── EC_Li_extracted.xml │ ├── EC_Li_mpid.xml │ ├── EC_extracted.xml │ ├── example_3_extract_residue_xml.py │ ├── example_4_convert_admp_to_mpid_Version2.py │ └── mpid_EC_DMC_extracted.xml ├── rename_opls.py ├── run_dmff.py └── run_mpid.py ├── md_phyneo ├── SAPT_to_json.py ├── __pycache__ │ └── mol_smiles.cpython-310.pyc ├── ase-md-example │ ├── energy_output.txt │ ├── err │ ├── gnn.py │ ├── graph.py │ ├── init.pdb │ ├── log │ ├── npt.log │ ├── npt.traj │ ├── npt.xyz │ ├── out │ ├── params_sgnn.pickle │ ├── params_sgnn_ABn.pickle │ ├── phyneo_ecl.xml │ ├── run_dmff_ase.py │ ├── sub.sh │ └── sub.sh.bj ├── create_mapping_smiles.py ├── create_smiles_from_pdb.py ├── draw_smiles_grid.py ├── mol_smiles.py ├── molecules_grid.svg ├── old_dmff_backend │ ├── peo_cmd_old_dmff_backend │ │ ├── __pycache__ │ │ │ ├── driver.cpython-310.pyc │ │ │ └── eann.cpython-310.pyc │ │ ├── client_dmff.py │ │ ├── driver.py │ │ ├── eann.py │ │ ├── ff_files_peo │ │ │ ├── forcefield.xml │ │ │ ├── params.pickle │ │ │ ├── params_eann.pickle │ │ │ └── params_sgnn.pickle │ │ ├── gnn.py │ │ ├── init.pdb │ │ ├── init_init.pdb │ │ ├── input.xml │ │ ├── recenter.py │ │ ├── run_client_dmff.sh │ │ ├── run_server.sh │ │ ├── sub.sh │ │ └── test_dmff.py │ └── water_cmd_old_dmff_backend │ │ ├── .tmp.xml │ │ ├── 6_1.pdb │ │ ├── Soper_2000_298_OH │ │ ├── Soper_2000_298_OO │ │ ├── __pycache__ │ │ ├── driver.cpython-37.pyc │ │ ├── driver.cpython-39.pyc │ │ ├── eann.cpython-37.pyc │ │ ├── eann.cpython-39.pyc │ │ ├── eannref.cpython-39.pyc │ │ ├── intra.cpython-37.pyc │ │ └── intra.cpython-39.pyc │ │ ├── ana_rdf.py │ │ ├── classicalMD_OO.xvg │ │ ├── clear.sh │ │ ├── client_dmff.py │ │ ├── density_0.03338.pdb │ │ ├── density_0.03338_init.pdb │ │ ├── driver.py │ │ ├── eann.py │ │ ├── err │ │ ├── forcefield.xml │ │ ├── former │ │ ├── input.xml │ │ ├── intra.py │ │ ├── out │ │ ├── params_eann.pickle │ │ ├── rdf.png │ │ ├── residues.xml │ │ ├── run_client_dmff.sh │ │ ├── run_server.sh │ │ ├── sub.sh │ │ └── test_ene.py ├── params_file │ ├── eapnn.py │ ├── new_model.tar │ ├── new_model │ │ ├── jnp2np.py │ │ ├── np2jnp.py │ │ ├── peg │ │ │ ├── __pycache__ │ │ │ │ ├── driver.cpython-310.pyc │ │ │ │ ├── eann.cpython-310.pyc │ │ │ │ ├── gnn.cpython-310.pyc │ │ │ │ └── graph.cpython-310.pyc │ │ │ ├── _params.pickle │ │ │ ├── _params_eann.pickle │ │ │ ├── _params_sgnn.pickle │ │ │ ├── client_dmff.py │ │ │ ├── driver.py │ │ │ ├── eann.py │ │ │ ├── forcefield.xml │ │ │ ├── gnn.py │ │ │ ├── graph.py │ │ │ ├── init.pdb │ │ │ ├── init_init.pdb │ │ │ ├── output.xml │ │ │ ├── params.npy │ │ │ ├── params.pickle │ │ │ ├── params_eann.npy │ │ │ ├── params_eann.pickle │ │ │ ├── params_sgnn.npy │ │ │ ├── params_sgnn.pickle │ │ │ ├── peg.xml │ │ │ └── test_dmff.py │ │ ├── peo │ │ │ ├── __pycache__ │ │ │ │ ├── driver.cpython-310.pyc │ │ │ │ ├── eann.cpython-310.pyc │ │ │ │ ├── gnn.cpython-310.pyc │ │ │ │ └── graph.cpython-310.pyc │ │ │ ├── _params.pickle │ │ │ ├── _params_eann.pickle │ │ │ ├── _params_sgnn.pickle │ │ │ ├── client_dmff.py │ │ │ ├── driver.py │ │ │ ├── eann.py │ │ │ ├── forcefield.xml │ │ │ ├── gnn.py │ │ │ ├── graph.py │ │ │ ├── init.pdb │ │ │ ├── init_init.pdb │ │ │ ├── output.xml │ │ │ ├── params.npy │ │ │ ├── params.pickle │ │ │ ├── params_eann.npy │ │ │ ├── params_eann.pickle │ │ │ ├── params_sgnn.npy │ │ │ ├── params_sgnn.pickle │ │ │ ├── peo.xml │ │ │ └── test_dmff.py │ │ └── test_dmff.py │ └── save2xml.py ├── peg_cmd │ ├── __pycache__ │ │ ├── driver.cpython-310.pyc │ │ ├── eann.cpython-310.pyc │ │ ├── gnn.cpython-310.pyc │ │ └── graph.cpython-310.pyc │ ├── _params.pickle │ ├── _params_eann.pickle │ ├── _params_sgnn.pickle │ ├── client_dmff.py │ ├── driver.py │ ├── eann.py │ ├── gnn.py │ ├── graph.py │ ├── init.pdb │ ├── init_init.pdb │ ├── peg.xml │ ├── run_client_dmff.sh │ ├── run_server.sh │ ├── sub.sh │ └── test_dmff.py └── peo_cmd │ ├── __pycache__ │ ├── driver.cpython-310.pyc │ ├── eann.cpython-310.pyc │ ├── gnn.cpython-310.pyc │ └── graph.cpython-310.pyc │ ├── _params.pickle │ ├── _params_eann.pickle │ ├── _params_sgnn.pickle │ ├── client_dmff.py │ ├── driver.py │ ├── eann.py │ ├── gnn.py │ ├── graph.py │ ├── init.pdb │ ├── init_init.pdb │ ├── peo.xml │ ├── run_client_dmff.sh │ ├── run_server.sh │ ├── sub.sh │ └── test_dmff.py ├── notebook ├── .ipynb_checkpoints │ └── phyneo-checkpoint.ipynb ├── peo │ ├── data.pickle │ ├── data_lr.pickle │ ├── data_sr.pickle │ ├── dataset_test_peo7_remove_nb.pickle │ ├── dataset_test_remove_nb.pickle │ ├── dataset_train_remove_nb.pickle │ ├── forcefield.xml │ ├── log │ ├── nn.err │ ├── params.pickle │ ├── params_sgnn.pickle │ ├── peo1.pdb │ ├── peo1_dimer.pdb │ ├── peo3.pdb │ ├── peo7.pdb │ ├── test_data.png │ ├── test_data.xvg │ └── test_data_pe16.xvg ├── peo3topeo7.jpg ├── phyneo.ipynb └── workflow.png ├── requirements.txt └── workflow ├── GNN_bonding ├── abinitio_intra │ ├── combine_sets.py │ ├── gen_inputs.py │ ├── mp2_template.com │ ├── pe.xml │ ├── pe8.pdb │ ├── run_md.py │ ├── serialize.py │ ├── set000.pickle │ ├── set001.pickle │ ├── set002.pickle │ ├── set003.pickle │ ├── set004.pickle │ ├── set005.pickle │ ├── set006.pickle │ ├── set007.pickle │ ├── set008.pickle │ └── set009.pickle ├── abinitio_intra_highT │ ├── combine_sets.py │ ├── gen_inputs.py │ ├── mp2_template.com │ ├── pe.xml │ ├── pe8.pdb │ ├── run_md.py │ ├── serialize.py │ ├── set000.pickle │ ├── set001.pickle │ ├── set002.pickle │ ├── set003.pickle │ ├── set004.pickle │ ├── set005.pickle │ ├── set006.pickle │ ├── set007.pickle │ ├── set008.pickle │ └── set009.pickle ├── abinitio_intra_pe16 │ ├── gen_inputs.py │ ├── mp2_template.com │ ├── pe.xml │ ├── pe16.pdb │ ├── run_md.py │ ├── serialize.py │ └── set.pickle ├── creat_dataset.py ├── dataset_test.pickle ├── dataset_test_pe16.pickle ├── dataset_test_pe16_remove_nb.pickle ├── dataset_test_remove_nb.pickle ├── dataset_train.pickle ├── dataset_train_remove_nb.pickle ├── nn.err ├── output.xml ├── params_sgnn.pickle ├── pe16.pdb ├── pe8.pdb ├── plot_data.py ├── remove_nonbonding.py ├── test_data.png ├── test_data.xvg ├── test_data_pe16.png ├── test_data_pe16.xvg ├── test_pe16.py └── train.py ├── lr_param ├── 1_gen_atype.py ├── 2_ff_gen.py ├── DMC.pdb ├── DMC.xyz ├── __pycache__ │ ├── convert_mom_to_xml.cpython-39.pyc │ ├── genkzkxky4xml.cpython-39.pyc │ ├── reformat_mom.cpython-39.pyc │ └── symmetrize_param.cpython-39.pyc ├── atype_data.pickle ├── axes ├── conf.DMC │ ├── input.clt │ └── input │ │ ├── OUT │ │ └── input_ISA-GRID.mom │ │ ├── input_ref_wt3_L2iso_000.out │ │ └── input_ref_wt3_L2iso_Cniso.pot ├── convert_mom_to_xml.py ├── dmff_forcefield.xml ├── genkzkxky4xml.py ├── localframe ├── pdbxyz ├── poledit ├── reformat_axes.py ├── reformat_mom.py └── symmetrize_param.py ├── md_pe ├── RESTART ├── __pycache__ │ └── driver.cpython-310.pyc ├── bulk.inp ├── bulk.pdb ├── client_dmff.py ├── driver.py ├── init_init.pdb ├── input.xml ├── log_dmff ├── logfile ├── make_init_pdb.py ├── params_sgnn.pickle ├── pe.xml ├── pe8.pdb ├── run_client_dmff.sh ├── run_server.sh ├── simulation.out ├── simulation.restart ├── sub.sh └── test_bulk │ ├── 1_make_elem_info.py │ ├── bulk.pdb │ ├── params_sgnn.pickle │ ├── pe.xml │ ├── pe8.pdb │ └── run.py ├── postprocess ├── README_MSD_Conductivity.md ├── USAGE_EXAMPLES_CN.md ├── ana_openmm_traj_rdf.py ├── calculate_msd_conductivity.py ├── example_usage.sh ├── gen_md_pdb.py ├── gen_nvt_init_pdb.py ├── get_msd_and_cond.py ├── get_msd_cond.py ├── get_msd_cond_travis.py ├── get_msd_mda_ipi.py ├── get_tcf_cond.py ├── get_tcf_diffcoeff.py ├── plot_rdf.py ├── plot_tcf_diffcoeff.py └── plot_travis_rdf.py └── sr_param ├── abinitio ├── geoms_op.py ├── gjfs │ └── 000 │ │ ├── 000.gjf │ │ ├── 001.gjf │ │ ├── 002.gjf │ │ ├── 003.gjf │ │ ├── 004.gjf │ │ ├── 005.gjf │ │ ├── 006.gjf │ │ ├── 007.gjf │ │ ├── 008.gjf │ │ ├── 009.gjf │ │ ├── 010.gjf │ │ └── 011.gjf ├── grep_mp2_res.sh ├── make_dimer.py ├── mp2 │ └── 000 │ │ ├── 000.com │ │ ├── 001.com │ │ ├── 002.com │ │ ├── 003.com │ │ ├── 004.com │ │ ├── 005.com │ │ ├── 006.com │ │ ├── 007.com │ │ ├── 008.com │ │ ├── 009.com │ │ ├── 010.com │ │ └── 011.com ├── mp2_template.com ├── mp2f12_template.com ├── opt.xyz ├── output.pdb ├── pdb │ └── 000 │ │ ├── 000.pdb │ │ ├── 001.pdb │ │ ├── 002.pdb │ │ ├── 003.pdb │ │ ├── 004.pdb │ │ ├── 005.pdb │ │ ├── 006.pdb │ │ ├── 007.pdb │ │ ├── 008.pdb │ │ ├── 009.pdb │ │ ├── 010.pdb │ │ └── 011.pdb ├── pe6_dimer.pdb ├── run_md.py ├── sapt │ ├── 000 │ │ ├── 000.com │ │ ├── 001.com │ │ ├── 002.com │ │ ├── 003.com │ │ ├── 004.com │ │ ├── 005.com │ │ ├── 006.com │ │ ├── 007.com │ │ ├── 008.com │ │ ├── 009.com │ │ ├── 010.com │ │ └── 011.com │ ├── data.pickle │ └── pack_data.py └── sapt_template.com ├── data.pickle ├── data_lr.pickle ├── data_sr.pickle ├── dimer └── pe6_dimer.pdb ├── 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