{"action":"created","issue":{"url":"https://api.github.com/repos/omnia-md/omnia-md/issues/13","labels_url":"https://api.github.com/repos/omnia-md/omnia-md/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/omnia-md/omnia-md/issues/13/comments","events_url":"https://api.github.com/repos/omnia-md/omnia-md/issues/13/events","html_url":"https://github.com/omnia-md/omnia-md/issues/13","id":58812373,"number":13,"title":"Command line application","user":{"login":"leeping","id":1441560,"avatar_url":"https://avatars.githubusercontent.com/u/1441560?v=3","gravatar_id":"","url":"https://api.github.com/users/leeping","html_url":"https://github.com/leeping","followers_url":"https://api.github.com/users/leeping/followers","following_url":"https://api.github.com/users/leeping/following{/other_user}","gists_url":"https://api.github.com/users/leeping/gists{/gist_id}","starred_url":"https://api.github.com/users/leeping/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/leeping/subscriptions","organizations_url":"https://api.github.com/users/leeping/orgs","repos_url":"https://api.github.com/users/leeping/repos","events_url":"https://api.github.com/users/leeping/events{/privacy}","received_events_url":"https://api.github.com/users/leeping/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":50,"created_at":"2015-02-24T21:58:54Z","updated_at":"2015-02-25T14:24:21Z","closed_at":null,"body":"This thread is to discuss adding an OpenMM command line application to Omnia, so that people can run OpenMM from the command line instead of writing a script.  Robert and I wrote a package which is a possible candidate:\r\n\r\nhttps://github.com/rmcgibbo/openmm-cmd\r\n\r\nCurrently, this code allows me to run OpenMM MD simulations from the command line without writing a Python script.  The range of simulations it can handle include the ten examples:\r\n\r\n1) Example PDB with AMBER\r\n2) Example PDB with AMOEBA\r\n3) Example PDB with system XML\r\n4) Example PDB with restart file\r\n5) iAMOEBA water box\r\n6) Acetophenone in AMOEBA water with system XML\r\n7) DHFR in explicit solvent\r\n8) DHFR in implicit solvent\r\n9) iAMOEBA ice-water interface with anisotropic barostat (requires latest OpenMM development version)\r\n10) Cox2 protein in implicit solvent, taken from AMBER examples.\r\n\r\nOur discussion should include whether this piece of code is sufficiently ready to include in Omnia, which would certainly spur further development.  The other option is to orphan this code and go with another option.  \r\n\r\nPersonally I am happy with any option as long as we end up with some command line application.  I strongly feel that adding the ability to run OpenMM from the command line would have a positive impact on our users."},"comment":{"url":"https://api.github.com/repos/omnia-md/omnia-md/issues/comments/75967540","html_url":"https://github.com/omnia-md/omnia-md/issues/13#issuecomment-75967540","issue_url":"https://api.github.com/repos/omnia-md/omnia-md/issues/13","id":75967540,"user":{"login":"swails","id":779022,"avatar_url":"https://avatars.githubusercontent.com/u/779022?v=3","gravatar_id":"","url":"https://api.github.com/users/swails","html_url":"https://github.com/swails","followers_url":"https://api.github.com/users/swails/followers","following_url":"https://api.github.com/users/swails/following{/other_user}","gists_url":"https://api.github.com/users/swails/gists{/gist_id}","starred_url":"https://api.github.com/users/swails/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/swails/subscriptions","organizations_url":"https://api.github.com/users/swails/orgs","repos_url":"https://api.github.com/users/swails/repos","events_url":"https://api.github.com/users/swails/events{/privacy}","received_events_url":"https://api.github.com/users/swails/received_events","type":"User","site_admin":false},"created_at":"2015-02-25T14:24:21Z","updated_at":"2015-02-25T14:24:21Z","body":"Ah, got it.  I still don't know what \"siegetank\" or \"FAH cores\" really are, though..."}}