md-analysis-tools

Scripts for molecular dynamics analysis, machine learning on MD data, GROMACS plotting, and HPC/Slurm job management.

molecular_dynamics/

Script	Language	Description
dihedral_angle_calculation	Python	Compute backbone and side-chain dihedral angles from MD trajectories
free_energy_surface_2d	Python	Build 2D free energy surfaces from `.npy` coordinate arrays
kl_divergence_bootstrapping	Python	KL divergence with bootstrapped confidence intervals between two MD ensembles
muller_potential_2d	Python	Müller-Brown potential energy surface for 2D sampling benchmarks
pdb_standardizer	Python	Strict PDB formatter with field-level validation and logging
tica_calculation	Python	Compute time-lagged independent components (TICs) from MD trajectories

Script	Language	Description
find_best_checkpoint	Python	Scans PyTorch Lightning `metrics.csv` logs and symlinks the best checkpoint
kl_divergence	Python	2D KL divergence between two datasets using kernel density estimation
kl_divergence_bootstrapping	Python	KL divergence with bootstrapped confidence intervals
Bootstrapping	Python	Bootstrapping utility for computing confidence intervals on arbitrary metrics

Script	Language	Description
xvg_line_graph	Python	Plot GROMACS `.xvg` files as line graphs
xvg_scatter_line	Python	Plot GROMACS `.xvg` files as combined scatter + line time series

Script	Language	Description
check_queue	Bash	Show your Slurm jobs with readable status summary
slurm_array_template	Bash	Ready-to-use Slurm array job template
submit_many_jobs	Bash	Submit `sbatch` jobs across many folders in one command
run_slurm_every_folder	Bash	Run a Slurm job inside every simulation subfolder (range or list mode)
search_slurm_logs	Bash	Search Slurm output logs for best metric values
gather_files	Bash	Collect files matching a pattern from a directory tree into one place
lineforge	Bash	Safe batch line replacement across files (dry-run, backup, regex support)

pip install -r requirements.txt

The Bash scripts have no Python dependencies. They require Bash and a Slurm-enabled HPC cluster for the hpc/ scripts.