{"id":19339526,"url":"https://github.com/becksteinlab/alchemical_conformational_analysis","last_synced_at":"2026-06-22T09:32:01.328Z","repository":{"id":137557674,"uuid":"380097986","full_name":"Becksteinlab/alchemical_conformational_analysis","owner":"Becksteinlab","description":null,"archived":false,"fork":false,"pushed_at":"2021-09-11T00:56:00.000Z","size":5845,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-09T14:33:02.131Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"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":null,"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":"2021-06-25T02:02:03.000Z","updated_at":"2022-06-30T19:06:40.000Z","dependencies_parsed_at":null,"dependency_job_id":"b934719b-de1b-4b00-b1df-40a04f11c54d","html_url":"https://github.com/Becksteinlab/alchemical_conformational_analysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Becksteinlab/alchemical_conformational_analysis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Falchemical_conformational_analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Falchemical_conformational_analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Falchemical_conformational_analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Falchemical_conformational_analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/alchemical_conformational_analysis/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Falchemical_conformational_analysis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34643587,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-22T02:00:06.391Z","response_time":106,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2024-11-10T03:22:42.352Z","updated_at":"2026-06-22T09:32:01.311Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Conformational Analysis of SAMPL7 molecules\n\nStart with SM46 (see submitted paper).\n\nBogdan created timeseries for the two main dihedrals (see tar file on spudda,\ntoo big for repo).\n\nTo set up:\n\n    bash ./bin/RSYNC\n    bash ./bin/SETUP\n\nYou can then use the notebooks in analysis.\n\nYou need a conda environment with\n\n- alchemlyb\n- pandas\n- matplotlib\n- numpy\n- tqdm\n- seaborn\n\n\n\n## Raw data\n\nGenerated with `gmx angle` (see `GROMACS_ANALYZE_dihedral_analysis`):\n```bash\n  gmx angle -type dihedral -f $i/md.xtc -n $ff-dih1.ndx -od $j-dih1-dist.xvg -ov $j-dih1-ts.xvg\n  gmx angle -type dihedral -f $i/md.xtc -n $ff-dih2.ndx -od $j-dih2-dist.xvg -ov $j-dih2-ts.xvg\n```\n\n### CGENFF and OPLS-AA (mol2ff)\n\nTar file with data. \n* `spudda.beckstein.physics.asu.edu:/nfs/homes/bogdan/Projects/SAMPL7-PhysProp/_dih_analysis.tgz`\n\nUse `bin/RSYNC.sh` to get the data.\n\n### GAFF and LigParGen\n\nShujie generated the data\n\n* `yamsolo.beckstein.physics.asu.edu:/nfs/homes3/sfan/Projects/SAMPL7/_dih_gaff`\n* `yamsolo.beckstein.physics.asu.edu:/nfs/homes3/sfan/Projects/SAMPL7/_dih_ligpargen`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Falchemical_conformational_analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Falchemical_conformational_analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Falchemical_conformational_analysis/lists"}