{"id":19339559,"url":"https://github.com/becksteinlab/adkgromacstutorial","last_synced_at":"2025-04-23T02:30:50.075Z","repository":{"id":137557597,"uuid":"65952370","full_name":"Becksteinlab/AdKGromacsTutorial","owner":"Becksteinlab","description":"Basic tutorial for running and analyzing a Gromacs MD simulation of AdK","archived":false,"fork":false,"pushed_at":"2018-07-03T15:03:07.000Z","size":23107,"stargazers_count":9,"open_issues_count":4,"forks_count":7,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-02T06:43:08.497Z","etag":null,"topics":["gromacs","molecular-dynamics-simulation","tutorial"],"latest_commit_sha":null,"homepage":"https://AdKGromacsTutorial.readthedocs.org","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Becksteinlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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}},"created_at":"2016-08-18T00:44:09.000Z","updated_at":"2024-06-03T22:47:15.000Z","dependencies_parsed_at":null,"dependency_job_id":"0275f2f7-ff12-4f33-8e34-feb8fd96db4b","html_url":"https://github.com/Becksteinlab/AdKGromacsTutorial","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FAdKGromacsTutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FAdKGromacsTutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FAdKGromacsTutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FAdKGromacsTutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/AdKGromacsTutorial/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250357558,"owners_count":21417306,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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","molecular-dynamics-simulation","tutorial"],"created_at":"2024-11-10T03:22:56.457Z","updated_at":"2025-04-23T02:30:50.064Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Shell","readme":"AdK Gromacs Tutorial\n====================\n\n[![docs](https://readthedocs.org/projects/adkgromacstutorial/badge/)](https://readthedocs.org/projects/adkgromacstutorial)\n\n\u003cimg src=\"/docs/figs/adk_secondary.jpg\" alt=\"Adenylate Kinase\" align=\"right\" width=\"200\"\u003e\n\nThe full tutorial is available online through\n[Read the Docs](http://adkgromacstutorial.readthedocs.io).\n\nObjective\n---------\n\nPerform an all-atom molecular dynamics (MD) simulation—using the [Gromacs]\nMD package—of the apo enzyme adenylate kinase (AdK) in its open conformation in\na physiologically realistic environment, and carry out a basic analysis of its\nstructural properties in equilibrium.\n\n\nTutorial files\n--------------\n\nAll of the necessary tutorial files can obtained by cloning the repository\n\n```bash\n  git clone https://github.com/Becksteinlab/AdKGromacsTutorial.git\n```\n\n\nWorkflow overview\n-----------------\n\nFor this tutorial we'll use [Gromacs] (version 5.1.3) to set up the system, run\nthe simulation, and perform analysis. An initial structure is provided, which\ncan be found in the :file:`tutorial/templates` directory, as well as the MDP\nfiles that are necessary for input to Gromacs. The overall workflow consists of\nthe following steps:\n\n1. Download tutorial files and set up working directories\n\n   - Obtain structure 4AKE from [PDB]\n   - Generate a stripped PDB file containing only chain A and no crystal waters\n\n2. Solvate the protein system\n\n   - Generate topology using default protonation states\n\n   - Solvate in water in simulation cell (rhombic dodecahedron)\n\n   - Ionize system with NaCl to neutralize and obtain physiological concentration\n\n3. Perform energy minimization\n\n4. Perform position-restrained equilibration\n\n5. Run production MD in the NPT ensemble\n\n6. Visualize the trajectory\n\n   - Center the protein in a box with primitive unitcell representation (periodic boundary conditions)\n\n   - RMS-fit the protein in each snapshot to the first snapshot\n\n\n[Gromacs]: http://www.gromacs.org\n[PDB]: http://www.rcsb.org/pdb/home/home.do\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fadkgromacstutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fadkgromacstutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fadkgromacstutorial/lists"}