StreaMD: a tool to perform high-throughput automated molecular dynamics simulations This is Apptainer (Singularity-compatible) container images providing a ready-to-run installation of StreaMD (CPU/GPU), a toolkit for high-throughput molecular dynamics (MD) simulations that automates preparation, equilibration, production, and analysis workflows for protein-only, protein–ligand, and protein–cofactor systems. Project resources Source code (GitHub): ci-lab-cz/streamd. GitHub Documentation (Read the Docs): StreaMD Documentation (overview, installation, CLI reference, config file, GBSA/MM-PBSA, ProLIF, etc.). Both streamd_cpu.sif and streamd_gpu.sif are built from the same StreaMD codebase (streamd version 0.4) and expose the same command-line interfaces (run_md, run_gbsa, run_prolif). All CLI options and parameters are identical between github version and CPU/GPU images; the only difference is runtime execution on GPU nodes, which requires --nv for the GPU image. streamd_cpu.sif (CPU container) This is an Apptainer CPU container image for StreaMD intended for execution on CPU nodes. Project resources Documentation (Read the Docs): StreaMD Documentation/cpu-usage. Usage apptainer exec --cleanenv streamd_cpu.sif run_md --help or apptainer run --cleanenv streamd_cpu.sif run_md --help or ./streamd_cpu.sif run_md --help Example: apptainer exec --cleanenv streamd_cpu.sif run_md -p protein.pdb -l ligand.mol --md_time 1 -d output_dir Advanced analysis tools: apptainer exec --cleanenv streamd_cpu.sif run_gbsa --help apptainer exec --cleanenv streamd_cpu.sif run_prolif --help StreaMD supports YAML configuration via --config (command-line arguments override config values). StreaMD Documentation/configurationThere is an option `-c/--ncpu` to control the number of CPUs used. By default all CPUs will be used.Example: apptainer exec --cleanenv streamd_cpu.sif run_md --config config.yml --ncpu 32 streamd_gpu.sif (GPU container) This is an Apptainer GPU container image for StreaMD intended for execution on NVIDIA GPU nodes. GPU runs should be launched with --nv to expose NVIDIA devices and driver libraries to the container. Project resources Documentation (Read the Docs): includes a dedicated section on GPU usage and runtime behavior. StreaMD Documentation/parallelism-and-gpus Usage on GPU nodes apptainer exec --nv --cleanenv streamd_gpu.sif run_md --help Example: apptainer exec --nv --cleanenv streamd_gpu.sif run_md -p protein.pdb -l ligand.mol --md_time 1 --device gpu