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md_analysis

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Name		Name	Last commit message	Last commit date
data		data
images		images
kinase		kinase
README.md		README.md
add_chain_id.py		add_chain_id.py
batch_remove.py		batch_remove.py
calpha_atom_distance.py		calpha_atom_distance.py
cluster.py		cluster.py
count.py		count.py
kinase.ipynb		kinase.ipynb
kinase_akt1.ipynb		kinase_akt1.ipynb
md.ipynb		md.ipynb
md.mdp.rtf		md.mdp.rtf
md.py		md.py
mdtraj_learning.ipynb		mdtraj_learning.ipynb
pdb2xtc_combine.py		pdb2xtc_combine.py
pdb_fix.py		pdb_fix.py
resnumber_change.py		resnumber_change.py
sel_protein.py		sel_protein.py
submit_all.sh		submit_all.sh
xtc2pdb.py		xtc2pdb.py

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MD simulation code for kinase simulation using OpenMM.

md.ipynb, md.py Run MD simulations

mda.ipynb Analyze simulation data

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