{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/openpathsampling/issues/482","repository_url":"https://api.github.com/repos/choderalab/openpathsampling","labels_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/482/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/482/comments","events_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/482/events","html_url":"https://github.com/choderalab/openpathsampling/pull/482","id":155485655,"number":482,"title":"[WIP] Alanine dipeptide TPS examples","user":{"login":"dwhswenson","id":8178546,"avatar_url":"https://avatars.githubusercontent.com/u/8178546?v=3","gravatar_id":"","url":"https://api.github.com/users/dwhswenson","html_url":"https://github.com/dwhswenson","followers_url":"https://api.github.com/users/dwhswenson/followers","following_url":"https://api.github.com/users/dwhswenson/following{/other_user}","gists_url":"https://api.github.com/users/dwhswenson/gists{/gist_id}","starred_url":"https://api.github.com/users/dwhswenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwhswenson/subscriptions","organizations_url":"https://api.github.com/users/dwhswenson/orgs","repos_url":"https://api.github.com/users/dwhswenson/repos","events_url":"https://api.github.com/users/dwhswenson/events{/privacy}","received_events_url":"https://api.github.com/users/dwhswenson/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"dwhswenson","id":8178546,"avatar_url":"https://avatars.githubusercontent.com/u/8178546?v=3","gravatar_id":"","url":"https://api.github.com/users/dwhswenson","html_url":"https://github.com/dwhswenson","followers_url":"https://api.github.com/users/dwhswenson/followers","following_url":"https://api.github.com/users/dwhswenson/following{/other_user}","gists_url":"https://api.github.com/users/dwhswenson/gists{/gist_id}","starred_url":"https://api.github.com/users/dwhswenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwhswenson/subscriptions","organizations_url":"https://api.github.com/users/dwhswenson/orgs","repos_url":"https://api.github.com/users/dwhswenson/repos","events_url":"https://api.github.com/users/dwhswenson/events{/privacy}","received_events_url":"https://api.github.com/users/dwhswenson/received_events","type":"User","site_admin":false},"milestone":null,"comments":8,"created_at":"2016-05-18T12:11:08Z","updated_at":"2016-05-22T15:31:39Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/openpathsampling/pulls/482","html_url":"https://github.com/choderalab/openpathsampling/pull/482","diff_url":"https://github.com/choderalab/openpathsampling/pull/482.diff","patch_url":"https://github.com/choderalab/openpathsampling/pull/482.patch"},"body":"This PR will include code for both of our alanine dipeptide TPS examples: fixed length and flexible length.\r\n\r\nFive new files. To reproduce results, run them in order:\r\n\r\n* `alanine_dipeptide_tps_first_traj.ipynb`: getting the first trajectory satisfying the flexible path length TPS approach\r\n* `alanine_dipeptide_tps.ipynb`: TPS for the flexible path length version\r\n* `alanine_dipeptide_fixed_tps_first_traj.ipynb`: Obtaining the first trajectory for the fixed path length TPS\r\n* `alanine_dipeptide_fixed_tps.ipynb`: TPS for the fixed path length version\r\n* `alanine_dipeptide_tps_analysis.ipynb`: Combined analysis file for fixed and flexible path length TPS.\r\n\r\n- [x] Get initial trajectory for AD example from hi temp\r\n- [x] Equilibrate in low temp path ensemble\r\n- [x] Run long flexible path length simulation\r\n- [x] Get fixed path length traj from flexible sim\r\n- [x] Run long fixed path length simulation\r\n- [ ] Analysis\r\n- [ ] Update ipynb directory readme\r\n\r\nIncludes parts of #481"},"comment":{"url":"https://api.github.com/repos/choderalab/openpathsampling/issues/comments/220838459","html_url":"https://github.com/choderalab/openpathsampling/pull/482#issuecomment-220838459","issue_url":"https://api.github.com/repos/choderalab/openpathsampling/issues/482","id":220838459,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"created_at":"2016-05-22T15:31:39Z","updated_at":"2016-05-22T15:31:39Z","body":"> Currently, yes. But here's the issue I was going to submit (already drafted) immediately after finishing this PR\r\n\r\nIt sounds like you'd like to just merge this partial PR and move right to the next PR then?  If so, then we can just discuss in that PR."}}
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