{"id":19695412,"url":"https://github.com/readdy/readdy-sim-starterkit","last_synced_at":"2026-06-17T14:32:36.445Z","repository":{"id":19225829,"uuid":"22460226","full_name":"readdy/readdy-sim-StarterKit","owner":"readdy","description":"This starter kit contains templates and necessary binaries to start simulating right away.","archived":false,"fork":false,"pushed_at":"2014-08-22T07:58:15.000Z","size":1420,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-02-27T12:45:14.895Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","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/readdy.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}},"created_at":"2014-07-31T07:18:06.000Z","updated_at":"2018-02-10T01:18:12.000Z","dependencies_parsed_at":"2022-08-01T03:08:47.432Z","dependency_job_id":null,"html_url":"https://github.com/readdy/readdy-sim-StarterKit","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/readdy/readdy-sim-StarterKit","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy-sim-StarterKit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy-sim-StarterKit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy-sim-StarterKit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy-sim-StarterKit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/readdy","download_url":"https://codeload.github.com/readdy/readdy-sim-StarterKit/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy-sim-StarterKit/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34453431,"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":"2026-06-17T02:00:05.408Z","response_time":127,"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":"2024-11-11T19:27:44.880Z","updated_at":"2026-06-17T14:32:36.428Z","avatar_url":"https://github.com/readdy.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"Welcome!\nGlad you intend to use ReaDDy for your particle-based reaction-diffusion simulations.\nThis is a quick starting package that sets you up right away.\n\nRun a simulation right away:\n\n1) go into simulation folder\n\u003e\tcd sim\n\n2) run the simulation\n\u003e\t./run.sh\n\nLook at the simulation\n\n1) download VMD:\n\u003e\t http://www.ks.uiuc.edu/Research/vmd/\n\n// if you are on a mac: open the .tcl script differently: Open VMD, click on 'File' in the upper left corner of the screen, click 'source' in the dropdown menu, and choose the StarterKitPath/sim/output/out_traj.xml.VMD.tcl to view it.\n\n2) have a look at your simulation trajectory:\n\u003e\tvmd -e output/out_traj.xml.VMD.tcl\n\n// The _bin_VMD-Visualizer automatically creates a vmd readable xyz trajectory from the readdy xml output and provides a VMD .tcl script to view it right away\n\n\nChange the simulation parameters:\n\nYou will find all simulation parameters in \n\u003e \tcd input\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freaddy%2Freaddy-sim-starterkit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Freaddy%2Freaddy-sim-starterkit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freaddy%2Freaddy-sim-starterkit/lists"}