├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── bin └── cg_spica ├── doc ├── Makefile ├── build │ └── html │ │ ├── .buildinfo │ │ ├── ENM.html │ │ ├── _downloads │ │ ├── 013e4c01db335200cc2735253f1ccb43 │ │ │ └── spica_db.prm │ │ ├── 01ea96c3cf4c97e1eb79bb03b1658e35 │ │ │ └── PARM.FILE │ │ ├── 14022ce587619f9f48d2aeea539f8b70 │ │ │ └── out.psf │ │ ├── 1a260e983dc98e6f15d47fe2d2b549e8 │ │ │ └── dopc.cg.pdb │ │ ├── 25310e5143479c4b4d54a57887abd994 │ │ │ └── WAT.top │ │ ├── 2dc9ad4d6e8f6c68e09661e6396164b0 │ │ │ └── CGindex.ndx │ │ ├── 3a6488a03aaeb7c18565975878e2a8ec │ │ │ └── out.psf │ │ ├── 3cb476d9e8b095e7bf140e430ec921ec │ │ │ └── molecule.itp │ │ ├── 3f844940f71883aeeef4a7b771cf347e │ │ │ └── 2mag.cg.top │ │ ├── 47fdcf09025d7bfb6d8eeb5a488a16ce │ │ │ └── prot_memb.cg.pdb │ │ ├── 5540ead703cd5cbb78ffd65d59ab1186 │ │ │ └── 1d6x.cg.top │ │ ├── 5f9083195e2926ec77c75c26f375c331 │ │ │ └── SPICA.itp │ │ ├── 600f82dc1cc23cb716a6ce5abb28d965 │ │ │ └── topol.top │ │ ├── 64e9f355d8aaed9eb3813e5a6dd949bf │ │ │ └── p_dopc.cg.pdb │ │ ├── 8e9cdde22baa024f4aff91f9c1e56f2d │ │ │ └── molecule.itp │ │ ├── 97d2d5bdacf640e6a19885f9a11c764a │ │ │ └── POPC.top │ │ ├── 9a6048a1be94fdccf49501ac7b3a06ac │ │ │ └── dopc.aa.pdb │ │ ├── acb6ef50e53365ffe7be54c2ac67a28e │ │ │ └── 2mag.cg.pdb │ │ ├── c2b106deaf88869d08cfdf2eb3bbd605 │ │ │ └── DOPC.top │ │ ├── dac3244e26aa141123a6aaa4f9295d9c │ │ │ └── topol.top │ │ ├── dea5c2693b8b198d339c1c55c8aec4ec │ │ │ └── CLA.top │ │ ├── ed47a3361a6d6b1c30c723bbb4f65945 │ │ │ └── SPICA.itp │ │ ├── f15f3bee47d070d3786d2188699f8d1e │ │ │ └── CGindex.ndx │ │ └── f5f5af490d7d980a588120e4bd0d510b │ │ │ └── DATA.FILE │ │ ├── _images │ │ ├── ENM_example.jpg │ │ ├── map2cg_example.jpg │ │ └── wat2polar_example.jpg │ │ ├── _sources │ │ ├── ENM.rst.txt │ │ ├── index.rst.txt │ │ ├── json2top.rst.txt │ │ ├── map2cg.rst.txt │ │ ├── maptraj.rst.txt │ │ ├── setup_gmx.rst.txt │ │ ├── setup_lmp.rst.txt │ │ └── wat2polar.rst.txt │ │ ├── _static │ │ ├── _sphinx_javascript_frameworks_compat.js │ │ ├── background_b01.png │ │ ├── basic.css │ │ ├── bizstyle.css │ │ ├── bizstyle.js │ │ ├── css3-mediaqueries.js │ │ ├── css3-mediaqueries_src.js │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── jquery-3.6.0.js │ │ ├── jquery.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.13.1.js │ │ └── underscore.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── json2top.html │ │ ├── map2cg.html │ │ ├── maptraj.html │ │ ├── objects.inv │ │ ├── search.html │ │ ├── searchindex.js │ │ ├── setup_gmx.html │ │ ├── setup_lmp.html │ │ └── wat2polar.html ├── make.bat └── source │ ├── ENM.rst │ ├── Go.rst │ ├── conf.py │ ├── data │ ├── .2mag.cg.top.pspica.swp │ ├── 2mag.aa.pdb │ ├── 2mag.cg.pdb │ ├── 2mag.cg.top │ ├── 2mag.cg.top.pspica │ ├── 2mag.cg.top.v1 │ ├── 2mag.cg.top.v1.Go │ ├── 2mag.cg.top.v2 │ ├── 2mag.cg.top.v2.Go │ ├── CGindex.ndx │ ├── CLA.top │ ├── DATA.FILE │ ├── DOPC.top │ ├── PARM.FILE │ ├── POPC.top │ ├── SPICA.itp │ ├── WAT.top │ ├── dopc.aa.pdb │ ├── dopc.cg.pdb │ ├── dssp.out │ ├── in.lammps │ ├── molecule.itp │ ├── out.psf │ ├── p_dopc.cg.pdb │ ├── setup_gmx_prot │ │ ├── 1d6x.cg.top │ │ ├── CGindex.ndx │ │ ├── minim.mdp │ │ ├── npt.mdp │ │ ├── out.psf │ │ ├── prot_memb.cg.200mM.pdb │ │ ├── prot_memb.cg.500mM.pdb │ │ ├── prot_memb.cg.pdb │ │ ├── table.xvg │ │ ├── table_LJ124W_SOLW.xvg │ │ ├── table_LJ96W_SOLW.xvg │ │ ├── table_SOLW_SOLW.xvg │ │ ├── topol.top │ │ └── toppar │ │ │ ├── 1d6x.cg.itp │ │ │ ├── CLA.itp │ │ │ ├── DOPC.itp │ │ │ ├── SPICA.itp │ │ │ └── WAT.itp │ ├── spica_db.prm │ ├── topol.top │ └── toppar │ │ ├── DOPC.itp │ │ ├── SPICA.itp │ │ └── WAT.itp │ ├── figures │ ├── ENM_example.jpg │ ├── dopc.aa.jpg │ ├── dopc.cg.jpg │ ├── map2cg_example.jpg │ ├── modion_fig.jpg │ ├── pspica_wat.jpg │ ├── spica_wat.jpg │ └── wat2polar_example.jpg │ ├── gen_gmxin.rst │ ├── gen_lmpin.rst │ ├── index.rst │ ├── 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