{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/perses/issues/175","repository_url":"https://api.github.com/repos/choderalab/perses","labels_url":"https://api.github.com/repos/choderalab/perses/issues/175/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/perses/issues/175/comments","events_url":"https://api.github.com/repos/choderalab/perses/issues/175/events","html_url":"https://github.com/choderalab/perses/pull/175","id":141405795,"number":175,"title":"[WIP] Geometry testsystems","user":{"login":"pgrinaway","id":4674712,"avatar_url":"https://avatars.githubusercontent.com/u/4674712?v=3","gravatar_id":"","url":"https://api.github.com/users/pgrinaway","html_url":"https://github.com/pgrinaway","followers_url":"https://api.github.com/users/pgrinaway/followers","following_url":"https://api.github.com/users/pgrinaway/following{/other_user}","gists_url":"https://api.github.com/users/pgrinaway/gists{/gist_id}","starred_url":"https://api.github.com/users/pgrinaway/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgrinaway/subscriptions","organizations_url":"https://api.github.com/users/pgrinaway/orgs","repos_url":"https://api.github.com/users/pgrinaway/repos","events_url":"https://api.github.com/users/pgrinaway/events{/privacy}","received_events_url":"https://api.github.com/users/pgrinaway/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":27,"created_at":"2016-03-16T21:20:35Z","updated_at":"2016-03-23T00:28:21Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/perses/pulls/175","html_url":"https://github.com/choderalab/perses/pull/175","diff_url":"https://github.com/choderalab/perses/pull/175.diff","patch_url":"https://github.com/choderalab/perses/pull/175.patch"},"body":"I'm adding additional tests for the `GeometryEngine` here. I've added tests that propose all lysozyme ligands to each other, as well as all kinase inhibitor ligands to each other."},"comment":{"url":"https://api.github.com/repos/choderalab/perses/issues/comments/200092826","html_url":"https://github.com/choderalab/perses/pull/175#issuecomment-200092826","issue_url":"https://api.github.com/repos/choderalab/perses/issues/175","id":200092826,"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":"2016-03-23T00:28:21Z","updated_at":"2016-03-23T00:28:21Z","body":"One other thought on \"how fast does this have to be?\": The primary criteria is how much computer effort is required to decorrelate in chemical space once the optimal relative free energies of different compounds are known. The metric of merit is the statistical inefficiency for hopping in compound space times the wall clock time per expanded ensemble iteration.  There are many ways to speed things up---including making the geometry proposal moves take longer but have higher acceptance probabilities via including more of the local environmental interactions in torsion proposals, parallel Monte Carlo, more clever NCMC pathways, etc.  But it there is low-hanging fruit---and a straightforward approach to speeding up torsion proposals might be one of them---this might be worth pursuing."}}