{"id":33069693,"url":"https://github.com/ci-lab-cz/streamd","last_synced_at":"2026-01-14T08:35:49.538Z","repository":{"id":43301300,"uuid":"462707005","full_name":"ci-lab-cz/streamd","owner":"ci-lab-cz","description":"Fully automated high-throughput MD pipeline","archived":false,"fork":false,"pushed_at":"2025-12-27T20:52:18.000Z","size":6848,"stargazers_count":86,"open_issues_count":6,"forks_count":16,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-12-28T11:58:22.133Z","etag":null,"topics":["gromacs","gromacs-tools","molecular-dynamics","molecular-dynamics-simulation"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ci-lab-cz.png","metadata":{"files":{"readme":"README.md","changelog":"changelog.md","contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-02-23T11:32:07.000Z","updated_at":"2025-12-27T20:52:21.000Z","dependencies_parsed_at":"2024-06-18T21:51:08.101Z","dependency_job_id":"7065cd06-780a-4b3a-8a3b-d8d2e21d76d9","html_url":"https://github.com/ci-lab-cz/streamd","commit_stats":null,"previous_names":["ci-lab-cz/streamd"],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/ci-lab-cz/streamd","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ci-lab-cz%2Fstreamd","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ci-lab-cz%2Fstreamd/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ci-lab-cz%2Fstreamd/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ci-lab-cz%2Fstreamd/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ci-lab-cz","download_url":"https://codeload.github.com/ci-lab-cz/streamd/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ci-lab-cz%2Fstreamd/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28414527,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T08:31:27.429Z","status":"ssl_error","status_checked_at":"2026-01-14T08:31:19.098Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["gromacs","gromacs-tools","molecular-dynamics","molecular-dynamics-simulation"],"created_at":"2025-11-14T09:00:24.205Z","updated_at":"2026-01-14T08:35:49.529Z","avatar_url":"https://github.com/ci-lab-cz.png","language":"Python","funding_links":[],"categories":["Molecular dynamics"],"sub_categories":["MD Engines-Frameworks"],"readme":"![StreaMD Logo](./streamd_logo.png)\n# StreaMD:  a tool to perform high-throughput automated molecular dynamics simulations\n\nStreaMD provides an end-to-end molecular dynamics workflow that takes a PDB structure as input and automatically performs system preparation, equilibration, production and continuation runs, and analysis,\nproducing XTC trajectories together with ready-to-use plots and CSV outputs.\n\n## Features:  \n- Run multiple simultaneous molecular dynamics simulations\n- Run multiple replicas of the same system for multiple complexes in a single command\n- Simulation for different systems:  \n    - Protein in Water;  \n    - Protein - Ligand;  \n    - Protein - Cofactor (multiple);  \n    - Protein - Ligand - Cofactor (multiple);  \n\n- Simulations of boron-containing molecules using Gaussian software\n- Simulations of ligand-binding metalloproteins with MCPB.py\n- Distributed computing using dask library\n- Running parallel simulations on multiple servers\n- Extending the time of MD simulations \n- Continuing interrupted MD simulations\n- Restarting interrupted MD preparation by invoking the same command\n- Implemented tools for end-state free energy calculations (gmx_MMPBSA) and protein–ligand interaction analysis (ProLIF)\n- Support for customized .mdp files\n- Interactive trajectory convergence analysis for multiple complexes\n- GPU support\n\n\n## Quick start\n```bash\n# Create environment (choose CPU-only or GPU)\nconda env create --file env.yml -n md          # or env_gpu.yml on GPU-capable hosts\nconda activate md\n\n# Install\npip install streamd\n# or latest main branch\npip install git+https://github.com/ci-lab-cz/streamd.git\n\n```\n   \n**Minimal protein-ligand run (1 ns)**\n```\nrun_md -p protein.pdb -l ligand.mol --md_time 1\n```\n   \n**Protein - multiple ligands multiple replicas runs (1 ns)**\n```\nrun_md -p protein.pdb -l ligands.sdf --md_time 1 --replicas 3 --seed 1024\n```\n  \n**Extend successfully finished simulations**\n```\nrun_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_*/ --md_time 10\n```\n    \n**GPU-accelerated simulations**\n```\nrun_md -p protein_HIS.pdb -l ligand.mol --md_time 1 --device gpu --ncpu 32\n```\n\nMore examples can be found in the [documentation](https://streamd.readthedocs.io/)\n\n\n## Documentation\nhttps://streamd.readthedocs.io/\n\n## License\nMIT\n\n## Ready-to-use containers (Apptainer)\nPre-built `.sif` images are available (CPU and GPU) in the [Zenodo record](https://zenodo.org/records/18176058)  \n**CPU:** `apptainer run --cleanenv streamd_cpu.sif run_md --help`  \n**GPU:** `apptainer run --nv --cleanenv streamd_gpu.sif run_md --help`\n\nThe provided `.sif` images are intended for Apptainer on Linux/HPC systems.\nGPU usage requires an NVIDIA GPU node and launching with `--nv` and `run_md --device gpu`.\n\n## Citation\nIvanova A, Mokshyna O, Polishchuk P.  \nStreaMD: the toolkit for high-throughput molecular dynamics simulations.  \n*J. Cheminf.* **2024**, 16 (1), 123.  \nhttps://doi.org/10.1186/s13321-024-00918-w","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fci-lab-cz%2Fstreamd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fci-lab-cz%2Fstreamd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fci-lab-cz%2Fstreamd/lists"}