GitHub - bussilab/saxs-md-gac

Material associated to Bernetti, Hall, and Bussi, arXiv:2103.04964

This notebook can be used to repeat the analysis and reproduce the figures reported in the manuscript.

Representative structures and cluster centroids are included (with solvent molecules).

Full trajectories at .

PLUMED Egg at

Name		Name	Last commit message	Last commit date
Latest commit History 18 Commits
input_files		input_files
README.md		README.md
allI_Hum_wallonratio_180ns_36001_redone.dat		allI_Hum_wallonratio_180ns_36001_redone.dat
allI_Hum_wallonratio_180ns_36001_redone_and_exVol.dat		allI_Hum_wallonratio_180ns_36001_redone_and_exVol.dat
allI_crys_wallonratio_180ns_36001.dat		allI_crys_wallonratio_180ns_36001.dat
allI_plum_36001.dat		allI_plum_36001.dat
avg_scan.dat		avg_scan.dat
bias_colvar_180ns_full		bias_colvar_180ns_full
cluster_centroids_zip.zip		cluster_centroids_zip.zip
colv_avg_scan.dat		colv_avg_scan.dat
colvar_all_atom_long		colvar_all_atom_long
colvar_martini_long		colvar_martini_long
colvar_rg_rmsd		colvar_rg_rmsd
crystal_after_mini_full_spectrum.dat		crystal_after_mini_full_spectrum.dat
gac_kcl.dat		gac_kcl.dat
gac_kcl_mgcl2.dat		gac_kcl_mgcl2.dat
longs_spectra.dat		longs_spectra.dat
notebookj_cleaned_for_SI.ipynb		notebookj_cleaned_for_SI.ipynb
shorts_spectra.dat		shorts_spectra.dat
solute_metad_compact.pdb		solute_metad_compact.pdb
solute_metad_extended_extreme.pdb		solute_metad_extended_extreme.pdb
solute_plainMD.pdb		solute_plainMD.pdb
starting_structure_metad.pdb		starting_structure_metad.pdb
vol_solv.dat		vol_solv.dat
vol_whole.dat		vol_whole.dat
xyz.dat		xyz.dat

Provide feedback