├── .github └── workflows │ └── swarmcg-tests.yml ├── .gitignore ├── CODEOWNERS ├── LICENSE.txt ├── README.md ├── environment.txt ├── environment.yml ├── images └── TOC_Swarm-CG_paper.png ├── itests ├── Dockerfile.base ├── Dockerfile.test └── entrypoint.sh ├── optimized_models_from_paper ├── BTA_Opti_exec_mode_1 │ ├── BTA.gro │ ├── BTA_CG_model_Opti_exec_mode_1.itp │ └── BTA_martini_v2.2P.itp ├── BTA_Opti_exec_mode_2 │ ├── BTA.gro │ ├── BTA_CG_model_Opti_exec_mode_2.itp │ └── BTA_martini_v2.2P.itp ├── BTT_Opti_exec_mode_1 │ ├── BTT.gro │ ├── BTT_CG_model_Opti_exec_mode_1.itp │ └── BTT_martini_v2.2P.itp ├── BTT_Opti_exec_mode_2 │ ├── BTT.gro │ ├── BTT_CG_model_Opti_exec_mode_2.itp │ └── BTT_martini_v2.2P.itp ├── Beta-cyclodextrin_Opti_exec_mode_1 │ ├── Beta-cyclodextrin.gro │ ├── Beta-cyclodextrin_CG_model_Opti_exec_mode_1.itp │ └── Beta-cyclodextrin_martini_v2.1_pc.itp ├── NDI_Opti_exec_mode_1 │ ├── NDI.gro │ ├── NDI_CG_model_Opti_exec_mode_1.itp │ ├── NDI_martini_v2.0_solvents.itp │ └── NDI_martini_v2.2_modified.itp ├── NDI_Opti_exec_mode_2 │ ├── NDI.gro │ ├── NDI_CG_model_Opti_exec_mode_2.itp │ ├── NDI_martini_v2.0_solvents.itp │ └── NDI_martini_v2.2_modified.itp ├── PAMAM-G1_Opti_exec_mode_1 │ ├── PAMAM-G1.gro │ ├── PAMAM-G1_CG_model_Opti_exec_mode_1.itp │ ├── PAMAM-G1_martini_v2.0_ions.itp │ └── PAMAM-G1_martini_v2.2_PEO_PS_CNP.itp ├── PAMAM-G2_Opti_exec_mode_1 │ ├── PAMAM-G2.gro │ ├── PAMAM-G2_CG_model_Opti_exec_mode_1.itp │ ├── PAMAM-G2_martini_v2.0_ions.itp │ └── PAMAM-G2_martini_v2.2_PEO_PS_CNP.itp ├── Pillar-5-arene_Opti_exec_mode_1 │ ├── Pillar-5-arene.gro │ ├── Pillar-5-arene_CG_model_Opti_exec_mode_1.itp │ ├── Pillar-5-arene_martini_v2.0_ions.itp │ └── Pillar-5-arene_martini_v2.2_PEO_PS_CNP.itp ├── Porphyrin_Opti_exec_mode_1 │ ├── Porphyrin.gro │ ├── Porphyrin_CG_model_Opti_exec_mode_1.itp │ ├── Porphyrin_martini_v2.0_solvents.itp │ └── Porphyrin_martini_v2.2_modified.itp ├── Porphyrin_Opti_exec_mode_2 │ ├── Porphyrin.gro │ ├── Porphyrin_CG_model_Opti_exec_mode_2.itp │ ├── Porphyrin_martini_v2.0_solvents.itp │ └── Porphyrin_martini_v2.2_modified.itp └── Spermine-dendron_Opti_exec_mode_1 │ ├── Spermine-dendron.gro │ ├── Spermine-dendron_CG_model_Opti_exec_mode_1.itp │ ├── Spermine-dendron_martini_v2.0_ions.itp │ └── Spermine-dendron_martini_v2.2_PEO_PS_CNP.itp ├── run-itest.sh ├── setup.py ├── swarmcg ├── __init__.py ├── analyze_optimization.py ├── config.py ├── data │ ├── equi.mdp │ ├── md.mdp │ └── mini.mdp ├── evaluate_model.py ├── io │ ├── __init__.py │ ├── job_args │ │ ├── __init__.py │ │ ├── analyze_config.py │ │ ├── defaults.py │ │ ├── evaluate_config.py │ │ └── optimize_config.py │ ├── read.py │ └── write.py ├── optimize_model.py ├── scoring │ ├── __init__.py │ ├── angles.py │ ├── bonds.py │ ├── dihedrals.py │ ├── distances.py │ ├── evaluation_function.py │ ├── rg.py │ └── sasa.py ├── shared │ ├── __init__.py │ ├── exceptions.py │ ├── math_utils.py │ ├── styling.py │ ├── utils.py │ └── validation.py ├── simulations │ ├── __init__.py │ ├── potentials.py │ ├── runner.py │ ├── settings.py │ ├── simulation_steps.py │ └── vs_functions.py ├── swarmCG.py └── utils.py └── tests ├── conftest.py ├── data ├── aa_topol.tpr ├── aa_traj.xtc ├── cg_map.ndx ├── cg_model.itp ├── cg_topol.tpr ├── cg_traj.xtc ├── martini_v2.0_PEO_PS_CNP.itp ├── martini_v2.0_ions.itp ├── start_conf.gro ├── system.top └── test.itp ├── io ├── job_args │ └── test_defaults.py └── test_read.py ├── shared ├── test_math_utils.py ├── test_utils.py └── test_validation.py └── simulations ├── test_runner.py ├── test_settings.py └── test_simulation_steps.py /.github/workflows/swarmcg-tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GMPavanLab/Swarm-CG/HEAD/.github/workflows/swarmcg-tests.yml -------------------------------------------------------------------------------- /.gitignore: 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