├── PorcupinePlot.tcl ├── README.md ├── gmx_install.md ├── gmx_mdp_files ├── ions.mdp ├── md.mdp ├── minim.mdp ├── npt.mdp └── nvt.mdp ├── gmx_mpi.sh ├── gmx_mpi_lab.md ├── modevectors.py ├── notes ├── metadynamics.md ├── 李毅笔记.md ├── 杜星笔记 ├── 梁晶步骤.txt └── 邓磊笔记.zip ├── thesis ├── fig_psd │ └── trimer.psd ├── fig_src │ ├── binding.jpg │ ├── dynamics.jpg │ ├── entry.png │ ├── metadynamics.png │ ├── microstate.png │ ├── nonbond.jpg │ └── trimer.jpg └── flexibility_and_transition.ppt ├── tips ├── PCAVAR.md ├── gnuplot.md ├── linux.md ├── openmm.md ├── plumed.md ├── pymol.md └── 表面电势.md ├── trajectory_analysis_by_Gromacs.md └── yhtest.ipynb /PorcupinePlot.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/liyigerry/gmx/HEAD/PorcupinePlot.tcl -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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