{"action":"created","issue":{"url":"https://api.github.com/repos/swails/ParmEd/issues/1","labels_url":"https://api.github.com/repos/swails/ParmEd/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/swails/ParmEd/issues/1/comments","events_url":"https://api.github.com/repos/swails/ParmEd/issues/1/events","html_url":"https://github.com/swails/ParmEd/pull/1","id":76484260,"number":1,"title":"OpenMM radians; factors of 2","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":5,"created_at":"2015-05-14T20:41:58Z","updated_at":"2015-05-14T21:55:02Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/swails/ParmEd/pulls/1","html_url":"https://github.com/swails/ParmEd/pull/1","diff_url":"https://github.com/swails/ParmEd/pull/1.diff","patch_url":"https://github.com/swails/ParmEd/pull/1.patch"},"body":"Hi Jason,\r\n\r\nThis pull request fixes a few things in agreement between Gromacs and OpenMM (for just one water molecule).  The problems appeared to be:\r\n\r\n1) Gromacs parser for \"angles\" and \"bonds\" were off by a factor of two in the force constant\r\n2) Degrees were being passed to OpenMM's angle force, but it expected radians\r\n\r\nMore to come soon.\r\n\r\n- Lee-Ping\r\n"},"comment":{"url":"https://api.github.com/repos/swails/ParmEd/issues/comments/102180973","html_url":"https://github.com/swails/ParmEd/pull/1#issuecomment-102180973","issue_url":"https://api.github.com/repos/swails/ParmEd/issues/1","id":102180973,"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},"created_at":"2015-05-14T21:55:02Z","updated_at":"2015-05-14T21:55:02Z","body":"Hi Jason,\r\n\r\nThe latest changes include a modification to the \"copy\" method in Atom to copy over the rmin and epsilon parameters if they're present.  Previously it was just copying the charge.\r\n\r\nAlso a factor of 2 was missing in the sigma -> rmin conversion.\r\n\r\nBefore:\r\n```\r\n#========================================================#\r\n#|              GROMACS energy components               |#\r\n#========================================================#\r\nLJ-(SR)                   [ 23.715675] \r\nCoulomb-(SR)              [-131.993668] \r\nPotential                 [-108.277992] \r\n----------------------------------------------------------\r\n#========================================================#\r\n#|         OpenMM energy components via ParmEd          |#\r\n#========================================================#\r\nHarmonicBondForce         6.07725467669e-12 \r\nNonbondedForce            -131.993509566 \r\nCMMotionRemover           0.0 \r\n----------------------------------------------------------\r\nForce Difference (kJ/mol/nm):\r\n[[  1.83117881e+02  -4.57891937e+02  -1.47315029e+02]\r\n [ -1.62929839e-03   8.91175780e-04  -3.72690559e-05]\r\n [  1.22881456e-03   1.32136416e-04  -6.26400553e-04]\r\n [ -1.24066323e+02   4.42464588e+02  -3.57819048e+02]\r\n [ -8.82529007e-04  -3.25313514e-05  -1.29761450e-03]\r\n [  8.29797175e-04   8.41101223e-04   1.62415667e-03]\r\n [  7.12609987e+00   4.16321009e+01   2.96937476e+02]\r\n [ -1.36539313e-04   4.11727609e-04  -1.73851815e-03]\r\n [  6.85973445e-04  -7.27411899e-04   1.47084107e-03]\r\n [  1.40309611e+02   1.24529203e+02  -7.76736053e+01]\r\n [ -2.31283720e-04   1.14568494e-03   1.19650037e-03]\r\n [  1.06758482e-03  -1.07080501e-03  -7.60351216e-04]\r\n [  3.97854290e+01   2.01726134e+02   1.46409046e+02]\r\n [  8.20437630e-04  -1.11976060e-03   9.12313427e-04]\r\n [ -5.60822908e-04   1.26041586e-03  -9.50374912e-04]\r\n [ -2.46274503e+02  -3.52461757e+02   1.39461602e+02]\r\n [ -4.20155016e-04  -1.31308867e-03  -8.64510380e-04]\r\n [  7.50836054e-04   1.44024189e-03   2.64969425e-04]]\r\n```\r\n\r\nAfter:\r\n```\r\ni#========================================================#\r\n#|              GROMACS energy components               |#\r\n#========================================================#\r\nLJ-(SR)                   [ 23.715675]\r\nCoulomb-(SR)              [-131.993668]\r\nPotential                 [-108.277992]\r\n----------------------------------------------------------\r\n#========================================================#\r\n#|         OpenMM energy components via ParmEd          |#\r\n#========================================================#\r\nHarmonicBondForce         6.07725467669e-12\r\nNonbondedForce            -108.277803748\r\nCMMotionRemover           0.0\r\n----------------------------------------------------------\r\nForce Difference (kJ/mol/nm):\r\n[[ -1.24241567e-04  -5.72125261e-04   3.22059995e-04]\r\n [ -1.62929839e-03   8.91175780e-04  -3.72690559e-05]\r\n [  1.22881456e-03   1.32136416e-04  -6.26400553e-04]\r\n [  8.62899257e-05  -1.03056918e-03   2.89419877e-04]\r\n [ -8.82529007e-04  -3.25313514e-05  -1.29761450e-03]\r\n [  8.29797175e-04   8.41101223e-04   1.62415667e-03]\r\n [ -5.44567355e-04   4.78497061e-04   4.54746908e-06]\r\n [ -1.36539313e-04   4.11727609e-04  -1.73851815e-03]\r\n [  6.85973445e-04  -7.27411899e-04   1.47084107e-03]\r\n [ -7.11152820e-04  -2.29622322e-04  -3.16007620e-04]\r\n [ -2.31283720e-04   1.14568494e-03   1.19650037e-03]\r\n [  1.06758482e-03  -1.07080501e-03  -7.60351216e-04]\r\n [ -5.99909368e-04  -9.03923662e-04  -3.85341403e-04]\r\n [  8.20437630e-04  -1.11976060e-03   9.12313427e-04]\r\n [ -5.60822908e-04   1.26041586e-03  -9.50374912e-04]\r\n [  8.77658510e-05   5.89657168e-04   5.25579499e-04]\r\n [ -4.20155016e-04  -1.31308867e-03  -8.64510380e-04]\r\n [  7.50836054e-04   1.44024189e-03   2.64969425e-04]]\r\n```\r\n\r\nThanks,\r\n\r\n- Lee-Ping"}}