{"id":26371645,"url":"https://github.com/sunghunbae/desmondtools","last_synced_at":"2026-01-03T12:34:55.442Z","repository":{"id":282127647,"uuid":"947554810","full_name":"sunghunbae/desmondtools","owner":"sunghunbae","description":"Tools for Schrodinger Desmond","archived":false,"fork":false,"pushed_at":"2025-03-12T23:57:47.000Z","size":705,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-13T00:20:01.843Z","etag":null,"topics":["desmond","dynamics","molecular","multisim","schrodinger"],"latest_commit_sha":null,"homepage":"https://sunghunbae.github.io/desmondtools/","language":"HTML","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/sunghunbae.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":"2025-03-12T21:55:26.000Z","updated_at":"2025-03-13T00:12:44.000Z","dependencies_parsed_at":"2025-03-13T00:30:07.744Z","dependency_job_id":null,"html_url":"https://github.com/sunghunbae/desmondtools","commit_stats":null,"previous_names":["sunghunbae/desmondtools"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sunghunbae%2Fdesmondtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sunghunbae%2Fdesmondtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sunghunbae%2Fdesmondtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sunghunbae%2Fdesmondtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sunghunbae","download_url":"https://codeload.github.com/sunghunbae/desmondtools/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243955718,"owners_count":20374372,"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":["desmond","dynamics","molecular","multisim","schrodinger"],"created_at":"2025-03-17T00:39:45.657Z","updated_at":"2026-01-03T12:34:55.437Z","avatar_url":"https://github.com/sunghunbae.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Tools for Desmond Molecular Dynamics\n\n## Introduction\n\nDesmondTools have a set of command-line scripts and a python library written to make \nsetting up the molecular dynamics simulations easier for Desmond.\n\n## Install\n\n```bash\n$ pip install desmondtools\n```\n\n## Documentation\n\nSee https://sunghunbae.github.io/desmondtools/\n\n\n## Use of `desmondtools` library\n\n```python\nfrom desmondtools import Multisim\n\n# read template .msj and .cfg\nmd_msj = Multisim(template=\"desmond-md.msj\")\nmd_cfg = Multisim(template=\"desmond-md.cfg\")\n\nwith open(msj_file,\"w\") as msj:\n    # modify desmond msj template\n    md_msj.dot.simulate[-1].cfg_file = cfg_file_basename\n    \n    # Setting up restraints using the restraints keyword:\n    # https://www.schrodinger.com/kb/332119\n    if args.posres_force \u003e 0.0:\n        # print the restraints in the multisim log file\n        md_msj.dot.simulate[-1].print_restraint = 'true'\n\n        # add the new terms defined in \"restraints.new\" to existing restraints.\n        # The default is restraints.existing = ignore which will \n        # delete existing terms before adding any new ones.\n        # md_msj.dot.simulate[-1].restraints.existing = 'retain'\n\n        md_msj.dot.simulate[-1].restraints.new = [\n            {\n                'name'              : 'posre_harm',\n                'atoms'             : [ f'\"{args.posres}\"' ],\n                'force_constants'   : [ args.posres_force, ] * 3,\n            }\n            ]\n        # force constants in the x, y, and z direction\n\n    md_msj.write(msj)\n\nwith open(cfg_file,\"w\") as cfg:\n    # modify desmond cfg template\n    md_cfg.dot.randomize_velocity.seed = random.randint(1000, 9999)\n    md_cfg.dot.time = total_simulation_time\n    md_cfg.dot.temperature = t_schedule\n    md_cfg.dot.trajectory.interval = args.interval\n    md_cfg.write(cfg)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsunghunbae%2Fdesmondtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsunghunbae%2Fdesmondtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsunghunbae%2Fdesmondtools/lists"}