{"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":54,"created_at":"2015-02-24T21:58:54Z","updated_at":"2015-02-25T17:03:02Z","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/76003050","html_url":"https://github.com/omnia-md/omnia-md/issues/13#issuecomment-76003050","issue_url":"https://api.github.com/repos/omnia-md/omnia-md/issues/13","id":76003050,"user":{"login":"peastman","id":4379786,"avatar_url":"https://avatars.githubusercontent.com/u/4379786?v=3","gravatar_id":"","url":"https://api.github.com/users/peastman","html_url":"https://github.com/peastman","followers_url":"https://api.github.com/users/peastman/followers","following_url":"https://api.github.com/users/peastman/following{/other_user}","gists_url":"https://api.github.com/users/peastman/gists{/gist_id}","starred_url":"https://api.github.com/users/peastman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peastman/subscriptions","organizations_url":"https://api.github.com/users/peastman/orgs","repos_url":"https://api.github.com/users/peastman/repos","events_url":"https://api.github.com/users/peastman/events{/privacy}","received_events_url":"https://api.github.com/users/peastman/received_events","type":"User","site_admin":false},"created_at":"2015-02-25T17:03:02Z","updated_at":"2015-02-25T17:03:02Z","body":"> Exposing 3 options on the command-line is fine. Exposing a couple dozen of them is less-so, and begs (IMO) for some kind of alternative UI.\r\n\r\nEven for the C++ app it's more than three options.  You need to specify the three input XML files, the output file, the simulation length, the frequency at which to write frames, possibly options about other data to report as the simulation runs (the same options as StateDataReporter), etc.  It's a much shorter list than what the Python app will support, but still... is there any reason *not* to use identical methods to specify those options in both apps?\r\n\r\nThe way Lee-Ping's app works, the \"normal\" way to specify most of these options is with a parameter file, but you can also override any option with a command line flag.  That seems to me like an elegant solution.  And equally so for both the Python and C++ apps.\r\n\r\n> I'm still puzzled as to what output formats would be supported.\r\n\r\nIn most previous discussions, we've said it would support only DCD.  That's a pretty trivial format to write, so no need to introduce new dependencies for it.\r\n\r\n>  Could we at least support some form of compressed XML files?\r\n\r\nThat sounds like a good idea.  Allow the user to specify a zip file, in which case it reads the XML files from inside that?"}}