├── .gitignore ├── 15leu2x ├── Instructions.pdf └── input │ ├── 15leu2x.psf │ ├── 15leu2x.s0.equil.coor │ ├── 15leu2x.s0.pdb │ ├── 15leu2x.s1.equil.coor │ ├── 15leu2x.s1.pdb │ ├── 15leu2x.s2.equil.coor │ ├── 15leu2x.s2.pdb │ ├── 15leu2x.s3.equil.coor │ ├── 15leu2x.s3.pdb │ ├── 15leu2x.s4.equil.coor │ ├── 15leu2x.s4.pdb │ ├── 15leu2x.s5.equil.coor │ ├── 15leu2x.s5.pdb │ ├── 15leu2x.s6.equil.coor │ ├── 15leu2x.s6.pdb │ ├── 15leu2x.s7.equil.coor │ ├── 15leu2x.s7.pdb │ ├── 15leu2x.s8.equil.coor │ ├── 15leu2x.s8.pdb │ ├── 15leu2x.s9.equil.coor │ ├── 15leu2x.s9.pdb │ ├── README.txt │ ├── abf.namd │ ├── alpha_ideal_ref.xyz │ ├── calc_variables.tcl │ ├── clear_pbc.tcl │ ├── colvar_display.tcl │ ├── demo.tcl │ ├── demo.vmd │ ├── dist_orient.colvars.in │ ├── drag_1d.namd │ ├── drag_6d.namd │ ├── force_helical_structure.colvars.in │ ├── mtd_1d.namd │ ├── mtd_2d.namd │ ├── packing_angles.colvars.in │ ├── par_all36_prot.prm │ ├── plot_colvars_traj.py │ ├── quaternion2rmatrix.tcl │ ├── restrain_helixA.colvars.in │ ├── show_rotation_axis.tcl │ ├── show_variables.tcl │ └── unbind.namd ├── README.md ├── symmetric_DBC ├── AFEP.colvars ├── README.md ├── RFEP_vacuum.colvars ├── ref.pdb └── ref_vacuum.pdb └── tma-aco ├── Common ├── charmm │ ├── par_all22_prot.prm │ ├── par_all35_ethers.prm │ ├── par_all36_carb.prm │ ├── par_all36_cgenff.prm │ ├── par_all36_lipid.prm │ ├── par_all36_na.prm │ ├── par_all36_prot.prm │ ├── par_all36m_prot.prm │ ├── top_all22_prot.rtf │ ├── top_all35_ethers.rtf │ ├── top_all36_carb.rtf │ ├── top_all36_cgenff.rtf │ ├── top_all36_lipid.rtf │ ├── top_all36_na.rtf │ ├── top_all36_prot.rtf │ └── toppar_water_ions.str ├── common.namd ├── distance.colvars.in ├── tma-aco.ndx ├── tma-aco.pdb ├── tma-aco.psf ├── tma-aco.xsc └── write_index_file.tcl ├── README.md ├── abf └── abf.namd ├── mtd-ti └── mtd-ti.namd ├── mtd └── mtd.namd ├── smd-ti └── smd-ti.namd ├── smd └── smd.namd ├── test └── test.namd ├── us-ti └── us-ti.namd └── us └── us.namd /.gitignore: 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