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new branch to add md simulations of longer peptide #29

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506 changes: 373 additions & 133 deletions examples/parameterize_peptide/generate_peptide_input_files.ipynb
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383 changes: 339 additions & 44 deletions examples/parameterize_peptide/output/peptide_amber.parm7
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323 changes: 184 additions & 139 deletions examples/parameterize_peptide/output/peptide_amber.pdb
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157 changes: 93 additions & 64 deletions examples/parameterize_peptide/output/peptide_amber.rst7
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