{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/perses/issues/203","repository_url":"https://api.github.com/repos/choderalab/perses","labels_url":"https://api.github.com/repos/choderalab/perses/issues/203/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/perses/issues/203/comments","events_url":"https://api.github.com/repos/choderalab/perses/issues/203/events","html_url":"https://github.com/choderalab/perses/pull/203","id":151218349,"number":203,"title":"Implement CBMC and GHMC NCMC","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":"closed","locked":false,"assignee":null,"milestone":null,"comments":30,"created_at":"2016-04-26T19:24:05Z","updated_at":"2016-05-26T00:25:25Z","closed_at":"2016-05-25T21:54:31Z","pull_request":{"url":"https://api.github.com/repos/choderalab/perses/pulls/203","html_url":"https://github.com/choderalab/perses/pull/203","diff_url":"https://github.com/choderalab/perses/pull/203.diff","patch_url":"https://github.com/choderalab/perses/pull/203.patch"},"body":"WIP. @jchodera I was wondering if you have a chance if you can take a look at the NCMC GHMC integrator in this PR--not sure why it's failing the test. I'll continue with the CPF in the meantime."},"comment":{"url":"https://api.github.com/repos/choderalab/perses/issues/comments/221746138","html_url":"https://github.com/choderalab/perses/pull/203#issuecomment-221746138","issue_url":"https://api.github.com/repos/choderalab/perses/issues/203","id":221746138,"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":"2016-05-26T00:25:25Z","updated_at":"2016-05-26T00:25:25Z","body":"> That might have been my fault, turning alchemical_angles back on. Sorry.\r\n\r\nI think this might be a bug in https://github.com/choderalab/alchemy, since even setting the `lambda_angles` function to `1` (which should not soften any angles) causes the tests to fail!\r\n```\r\n======================================================================\r\nERROR: Testing alchemical null transformation of ALA sidechain in alanine dipeptide with 2 NCMC steps\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/nose/case.py\", line 197, in runTest\r\n    self.test(*self.arg)\r\n  File \"/Users/choderaj/github/choderalab/perses/perses.choderalab/perses/tests/test_elimination.py\", line 133, in check_alchemical_null_elimination\r\n    raise Exception(msg)\r\nException: Delta F (2 steps switching) = 6.493700 +- 0.317974 kT; should be within 6.000000 sigma of 0\r\ndelete logP:\r\n[-79.70428141 -80.83932505 -76.8615626  -82.60606613 -86.03060286\r\n -81.71043243 -80.0661826  -79.34087854 -80.38196626 -75.51265159\r\n -76.26955668 -73.4648813  -79.29217533 -79.97858927 -79.55299606\r\n -80.12284889 -82.80955511 -85.36092265 -83.69035794 -84.66686886\r\n -83.90630515 -78.46987044 -85.44788896 -86.59241216 -85.80761046\r\n -84.13009688 -86.05525829 -87.00567413 -81.8206416  -77.54424972\r\n -81.68716999 -78.20453923 -77.98520899 -82.79431237 -78.52813593\r\n -79.83464661 -87.91354246 -85.33079371 -74.97188706 -78.96469259\r\n -75.75294977 -76.18923385 -74.60409777 -78.56556047 -76.68058365\r\n -80.21437615 -76.74648416 -78.98927248 -74.30864834 -79.11703895]\r\ninsert logP:\r\n[ 72.74363482  73.23420777  68.10794608  75.86894404  81.53708021\r\n  72.76379023  71.91466909  72.8131977   71.60748884  67.95741827\r\n  66.3498206   64.2769053   60.06253775  75.70326373  75.31892855\r\n  69.42001191  74.29313664  73.00888961  75.50409717  79.52910367\r\n  76.10609788  69.25754533  74.16873518  82.02559285  77.6483282\r\n  69.26191363  77.75386101  80.86504407  75.54926068  65.09575461\r\n  74.72553539  70.39168886  69.09763387  76.23984347  66.672109\r\n  68.68338712  78.43566881  78.78423516  67.96189314  69.55944398\r\n  64.80455292  62.74293809  64.13150335  70.35453868  66.58393681\r\n  72.38839892  69.41483385  69.83439885  66.90193814  72.33572674]\r\nlogP:\r\n[ -6.9606466   -7.60511728  -8.75361652  -6.73712209  -4.49352265\r\n  -8.9466422   -8.15151352  -6.52768085  -8.77447741  -7.55524888\r\n  -9.91973608  -9.187976   -19.22963758  -4.27532554  -4.23406751\r\n -10.70283697  -8.51641847 -12.35203305  -8.18626077  -5.13776519\r\n  -7.80020727  -9.21232511 -11.27915379  -4.56683116  -8.15928226\r\n -14.86818324  -8.30139728  -6.14063006  -6.27138092 -12.4484951\r\n  -6.9616346   -7.81285038  -8.88757512  -6.55446891 -11.85602693\r\n -11.15125949  -9.47787365  -6.54655855  -7.00999391  -9.40524861\r\n -10.94839684 -13.44629576 -10.47259443  -8.21102179 -10.09664684\r\n  -7.82597723  -7.33165031  -9.15487363  -7.4067102   -6.78131221]\r\n```"}}
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