├── .gitignore ├── 1-MD_tutorial ├── 1-1-GMX_installation │ ├── README.md │ ├── cmake_GMX2021.2-CPU.sh │ ├── cmake_GMX2021.2-cuda.sh │ ├── cmake_GMX2021.3_CPU_double.sh │ ├── cmake_GMX2021.3_cuda.sh │ ├── cmake_GMX2022.4-CPU.sh │ └── downloadGMX.sh ├── 1-2-Amber_installation │ └── README.md ├── 1-3-force_field_bond_parameter │ ├── README.md │ ├── bond_param.ipynb │ ├── methane.gro │ ├── methane.top │ ├── nvt.log │ └── nvt.mdp ├── 1-4-force_field_non_bond │ ├── README.md │ ├── methane.gro │ ├── methane.pdb │ └── methane.top ├── 1-5-Antechamber-GAFF-non-standard-residue-prepare │ ├── 3HTB_clean.pdb │ ├── README.md │ ├── jz4.frcmod │ ├── jz4.gjf │ ├── jz4.log │ ├── jz4.mol2 │ ├── jz4.pdb │ ├── jz4_GMX.gro │ ├── jz4_GMX.top │ ├── jz4_pymol.mol2 │ ├── test.prmtop │ └── test.rst7 └── 1-6-Amber-protein-GAFF-ligand │ ├── 1-em │ ├── minim-FC-500.mdp │ └── minim-NoRes.mdp │ ├── 2-nvt │ └── nvt.mdp │ ├── 3-npt │ └── npt.mdp │ ├── 4-npt │ └── npt.mdp │ ├── README.md │ └── TOP │ ├── 3HTB_01.gro │ ├── 3HTB_02_complex.gro │ ├── 3HTB_clean.pdb │ ├── 3HTB_clean_pro.pdb │ ├── amber99sb-ildn_modify.ff │ └── ffnonbonded.itp │ ├── jz4.itp │ ├── jz4_GMX.gro │ ├── jz4_GMX.top │ ├── jz4_posres.itp │ ├── posre.itp │ └── topol.top ├── CC_news_008_ddG_uniFEP ├── GMX │ ├── 2zf0.pdb │ ├── 2zff.pdb │ ├── 2zff_02_tleap.pdb │ ├── amber14sb_parmbsc1.ff.tar.gz │ ├── ligand │ │ ├── MOL.itp │ │ ├── ffMOL.itp │ │ ├── ffMOL_dum.itp │ │ ├── ffmerged.itp │ │ ├── lig_3a │ │ │ ├── 51U_GMX.gro │ │ │ ├── 51U_GMX.top │ │ │ ├── MOL.itp │ │ │ ├── MOL.prmtop │ │ │ ├── MOL.rst7 │ │ │ ├── MOL_tleap.pdb │ │ │ ├── MOL_tleap_3a.pdb │ │ │ ├── atomtype.itp │ │ │ ├── lig.pdb │ │ │ ├── lig_H.frcmod │ │ │ ├── lig_H.mol2 │ │ │ └── lig_H.pdb │ │ ├── lig_5 │ │ │ ├── 53U_GMX.gro │ │ │ ├── 53U_GMX.top │ │ │ ├── MOL.itp │ │ │ ├── MOL.prmtop │ │ │ ├── MOL.rst7 │ │ │ ├── MOL_tleap.pdb │ │ │ ├── MOL_tleap_5.pdb │ │ │ ├── atomtype.itp │ │ │ ├── lig.pdb │ │ │ ├── lig_H.frcmod │ │ │ ├── lig_H.mol2 │ │ │ └── lig_H.pdb │ │ ├── merged.pdb │ │ ├── mergedB.pdb │ │ ├── pair.pse │ │ ├── pairs.dat │ │ └── tleap.in │ ├── pro │ │ ├── 08_ion.pdb │ │ ├── 2zff_03_pdb2gmx.pdb │ │ ├── 2zff_04_complex.pdb │ │ ├── amber14sb_parmbsc1.ff │ │ ├── posre_Protein.itp │ │ ├── posre_Protein2.itp │ │ ├── posre_Protein3.itp │ │ ├── posre_lig.itp │ │ ├── topol.top │ │ ├── topol_Protein.itp │ │ ├── topol_Protein2.itp │ │ ├── topol_Protein3.itp │ │ └── win24 │ │ │ ├── 0-creat.sh │ │ │ ├── 1-NVT_job.sh │ │ │ ├── 2-NPT-grompp.sh │ │ │ ├── 3-prod_MD.sh │ │ │ ├── em.mdp │ │ │ ├── md.mdp │ │ │ ├── npt_10.mdp │ │ │ ├── nvt.mdp │ │ │ └── result │ │ │ └── results.txt │ └── wat │ │ ├── 01_box.gro │ │ ├── 02_solv.gro │ │ ├── 04_ion_added.gro │ │ ├── em.mdp │ │ ├── topol.top │ │ └── win20-5ns │ │ ├── creat.sh │ │ ├── em.mdp │ │ ├── md.mdp │ │ ├── npt_10.mdp │ │ └── result │ │ └── results.txt ├── README.md ├── ligands.jpg └── uniFEP │ ├── 2zff_02_tleap.pdb │ ├── 2zff_03_tleap_chain.pdb │ ├── lig_3a │ └── lig_H_3a.sdf │ └── lig_5 │ └── lig_H_5.sdf ├── CC_news_009 ├── README.md └── mindmap.png ├── CC_news_011_replica_exchange ├── Langevin.py ├── Langevin_test.py ├── README.md ├── T_001 │ └── 900mmol │ │ └── 02-RE │ │ ├── md_0.mdp │ │ ├── nvt-eq.mdp │ │ ├── run_01.sh │ │ └── run_02_RE.sh ├── test_dstribution.py └── traj02 │ └── run_all.sh ├── CC_news_013_mdanalysis ├── 01-exe_time.png ├── README.md ├── data │ ├── fix_atom_c_40ps_short.xtc │ ├── index_CYS159-CYS284_PRO155-GLY280.ndx │ ├── md.tpr │ └── npt.pdb ├── plot.ipynb └── speed_test_distance │ ├── 01-mdtraj │ └── distance_iter.py │ ├── 02-mdanalysis │ └── distance_iter.py │ ├── 03-pytraj │ └── distance_iter.py │ ├── 04-GMX_distance │ └── distance.sh │ ├── 05-GMXLIB_CPP │ ├── CMakeLists.txt │ └── distance.cpp │ └── run_all.sh ├── CC_news_014_alchemical_pKa_calculation_and_error_cancellation ├── README.md ├── linear.png ├── pKa_matrix │ ├── Charmm36m │ │ ├── JOB │ │ │ ├── 01-pre-eq │ │ │ │ └── 01-em-all.sh │ │ │ ├── 02-PMX │ │ │ │ ├── run_01_eq.sh │ │ │ │ ├── run_02_check.sh │ │ │ │ ├── run_03_trjconv.sh │ │ │ │ ├── run_04_submit.sh │ │ │ │ ├── run_05_check_ne.sh │ │ │ │ └── run_06_integrate_and_BAR.sh │ │ │ └── 03-HRE │ │ │ │ ├── 01-L_opt │ │ │ │ ├── run_01_eq.sh │ │ │ │ ├── run_02_check.sh │ │ │ │ └── run_03_Lambda_opt.ipynb │ │ │ │ └── 02-win16 │ │ │ │ ├── run_04_prepare.sh │ │ │ │ ├── run_05_gro.sh │ │ │ │ ├── run_06_submit.sh │ │ │ │ ├── run_07_check.sh │ │ │ │ └── run_08_alchemical_analysis.sh │ │ ├── MDP │ │ │ └── genion.mdp │ │ ├── analysis │ │ │ └── fit_matrix.ipynb │ │ ├── pair.dat │ │ ├── run_01_prepare.sh │ │ ├── run_02_pdb2gmx.sh │ │ ├── run_03_gen_B.sh │ │ ├── run_04_top.sh │ │ ├── run_05_pdbbox.sh │ │ ├── run_06_ion.sh │ │ ├── run_08.sh │ │ └── tmp │ │ │ ├── 01-pre-eq │ │ │ ├── Lambda_0 │ │ │ │ ├── em.mdp │ │ │ │ └── npt.mdp │ │ │ └── Lambda_1 │ │ │ │ ├── em.mdp │ │ │ │ └── npt.mdp │ │ │ ├── res_CA.itp │ │ │ └── topol_tmp.top │ └── peptides_pdb_build │ │ ├── amber14sb │ │ ├── ASH.pdb │ │ ├── ASP.pdb │ │ ├── CYM.pdb │ │ ├── CYS.pdb │ │ ├── GLH.pdb │ │ ├── GLU.pdb │ │ ├── HID.pdb │ │ ├── HIE.pdb │ │ ├── HIP.pdb │ │ ├── LYN.pdb │ │ ├── LYS.pdb │ │ └── tleap.in │ │ └── charmm36m │ │ ├── ASP.pdb │ │ ├── ASPP.pdb │ │ ├── CYM.pdb │ │ ├── CYS.pdb │ │ ├── GLU.pdb │ │ ├── GLUP.pdb │ │ ├── HSD.pdb │ │ ├── HSE.pdb │ │ ├── HSP.pdb │ │ ├── LSN.pdb │ │ ├── LYS.pdb │ │ └── conver_pdb.sh ├── paper1.gif ├── paper2.gif ├── paper3.gif ├── paper4.gif └── paper5.gif ├── Chemshell └── Py-chemshell-installation │ └── README.md ├── README.md └── YuMuhan_Open_Course ├── MM-potential ├── 1-bond │ ├── 0.pdb │ ├── 0.png │ ├── 1.pdb │ ├── 1.png │ ├── 2.pdb │ ├── 2.png │ ├── bond.png │ └── bond.pse ├── 2-angle │ ├── 0.pdb │ ├── 0.png │ ├── 1.pdb │ ├── 1.png │ ├── 2.pdb │ ├── 2.png │ ├── angle.png │ └── angle.pse ├── 3-dihe │ ├── 0.pdb │ ├── 0.png │ ├── 1.pdb │ ├── 1.png │ ├── dihe.png │ └── dihe.pse ├── 4-vdw │ └── vdw.png ├── 5-coulomb │ └── Coulomb.png └── potential.ipynb ├── README.md └── gromacs蛋白模拟的力场简介.pdf /.gitignore: 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