├── .gitignore ├── LICENSE ├── README.md ├── examples ├── adp-free_energy_with-string.png ├── alanine-dipeptide │ ├── README.md │ ├── config.json │ ├── config_steered.json │ ├── config_string.json │ ├── mdp │ │ ├── plumed.dat │ │ ├── plumed_pull.dat │ │ ├── restrained.mdp │ │ ├── steered.mdp │ │ └── swarms.mdp │ ├── run_steered.sh │ ├── run_string.sh │ ├── strings │ │ ├── rescale_string.py │ │ ├── string0.txt │ │ ├── string0_long.txt │ │ ├── string0_radians.txt │ │ ├── string0_radians_scaled.txt │ │ ├── string0_short.txt │ │ └── string_intermediate.txt │ ├── submit_beskow.sh │ ├── submit_steered.sh │ ├── submit_string.sh │ ├── topology │ │ ├── end.gro │ │ ├── index.ndx │ │ ├── start.gro │ │ └── topol.top │ ├── visualize_free_energy_adp.py │ └── visualize_strings_adp.py ├── beta2 │ ├── README.md │ ├── config.json │ ├── md │ │ └── 0 │ │ │ ├── 0 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 1 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 2 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 3 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 4 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 5 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 6 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 7 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 8 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 9 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 10 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 11 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 12 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 13 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 14 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 15 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 16 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 17 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ ├── 18 │ │ │ └── restrained │ │ │ │ └── confout.gro │ │ │ └── 19 │ │ │ └── restrained │ │ │ └── confout.gro │ ├── mdp │ │ ├── restrained.mdp │ │ └── swarms.mdp │ ├── run_mpi.sh │ ├── run_omp.sh │ ├── strings │ │ ├── rescale_string.py │ │ ├── string0-scaled.txt │ │ └── string0.txt │ ├── submit_beskow.sh │ └── topology │ │ ├── end.gro │ │ ├── index.ndx │ │ ├── start.gro │ │ ├── topol.top │ │ └── toppar │ │ ├── CLA.itp │ │ ├── POPC.itp │ │ ├── PROA.itp │ │ ├── PROB.itp │ │ ├── SOD.itp │ │ ├── TIP3.itp │ │ └── charmm36.itp └── start-up │ ├── README.md │ ├── analyze_initial_string.ipynb │ ├── config.json │ ├── config_steered.json │ ├── environment.yml │ ├── input_maker.ipynb │ ├── md │ └── .gitkeep │ ├── mdp │ ├── restrained.mdp │ ├── steered.mdp │ └── swarms.mdp │ ├── slurm_out │ └── .gitkeep │ ├── slurm_steering_dardel.sh │ ├── slurm_string_dardel.sh │ ├── string_check.ipynb │ ├── strings │ └── .gitkeep │ └── topology │ ├── end.gro │ ├── index0.ndx │ ├── start.gro │ ├── topol.top │ └── toppar │ ├── CLA.itp │ ├── POPC.itp │ ├── PROA.itp │ ├── PROB.itp │ ├── SOD.itp │ ├── TIP3.itp │ └── charmm36.itp ├── stringmethod ├── __init__.py ├── config.py ├── main.py ├── postprocessing │ ├── __init__.py │ ├── base.py │ ├── cv_value_extraction.py │ ├── free_energy_calculation.py │ ├── index_conversion.py │ └── transition_count_calculation.py ├── simulations │ ├── __init__.py │ ├── gmx_jobs │ │ ├── __init__.py │ │ └── gmx_jobs.py │ ├── mdtools.py │ ├── steeredmd.py │ └── stringmd.py └── utils │ ├── __init__.py │ ├── custom.py │ ├── mdp_parser.py │ ├── scaling.py │ └── string_reparametrization.py └── tests └── test_processing.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/delemottelab/string-method-swarms-trajectories/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/delemottelab/string-method-swarms-trajectories/HEAD/LICENSE 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