{"action":"created","issue":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/152","labels_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/152/labels{/name}","comments_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/152/comments","events_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/152/events","html_url":"https://github.com/ParmEd/ParmEd/pull/152","id":78818340,"number":152,"title":"Gromacs support","user":{"login":"swails","id":779022,"avatar_url":"https://avatars.githubusercontent.com/u/779022?v=3","gravatar_id":"","url":"https://api.github.com/users/swails","html_url":"https://github.com/swails","followers_url":"https://api.github.com/users/swails/followers","following_url":"https://api.github.com/users/swails/following{/other_user}","gists_url":"https://api.github.com/users/swails/gists{/gist_id}","starred_url":"https://api.github.com/users/swails/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/swails/subscriptions","organizations_url":"https://api.github.com/users/swails/orgs","repos_url":"https://api.github.com/users/swails/repos","events_url":"https://api.github.com/users/swails/events{/privacy}","received_events_url":"https://api.github.com/users/swails/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":24,"created_at":"2015-05-21T04:09:59Z","updated_at":"2015-05-21T17:07:08Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ParmEd/ParmEd/pulls/152","html_url":"https://github.com/ParmEd/ParmEd/pull/152","diff_url":"https://github.com/ParmEd/ParmEd/pull/152.diff","patch_url":"https://github.com/ParmEd/ParmEd/pull/152.patch"},"body":"This PR adds full support for Gromacs topology files and GRO coordinate files to ParmEd.  It also adds a *lot* of other features designed during the process of supporting Gromacs and bug fixes for issues found while supporting Gromacs.  A most likely incomplete list:\r\n\r\n- Parse fully parametrized Gromacs topology files\r\n- Parse GRO files\r\n- Fix issue in which distance-based Amber masks would only work on AmberParm instances (now it works for all Structure instances)\r\n- Fix a buggy `update_dihedral_exclusions` method which is often useful when converting between formats\r\n- Fix some issues in `Structure` copying when splitting dihedrals\r\n- Assign parameters in CHARMM PSF files from a *copy* of the parameter set rather than the parameter set itself. This prevents multiple CHARMM PSF instances from claiming the same parameter type instances, which will cause problems (since they can only be \"bound\" to one list at a time).\r\n- Drastically improves slice performance for `Structure` (about 10x faster)\r\n- Implements split, `+`, and `*` for `Structure` complete with documentation\r\n- Adds Gromacs examples and updates existing examples to make sure it works correctly\r\n- Updates README with contributors\r\n- Update all OpenMM tests to work with the CPU platform, and update tolerances to reduce the occurrence of false failures\r\n\r\nAnything else I forgot?"},"comment":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/comments/104356962","html_url":"https://github.com/ParmEd/ParmEd/pull/152#issuecomment-104356962","issue_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/152","id":104356962,"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":"2015-05-21T17:07:07Z","updated_at":"2015-05-21T17:07:07Z","body":"I changed the .mdp settings to be a bit more reasonable.  Here are the answers I'm getting, if you'd like to check your numbers.\r\n\r\n```\r\n#========================================================#\r\n#|              GROMACS energy components               |#\r\n#========================================================#\r\nAngle                     1405.73542 \r\nProper-Dih.               236.932663 \r\nRyckaert-Bell.            428.05506 \r\nImproper-Dih.             33.201542 \r\nLJ-(SR)                   126.113748 \r\nDisper.-corr.             -425.915851 \r\nCoulomb-(SR)              -11792.257432 \r\nCoul.-recip.              -10122.51307 \r\nPotential                 -20110.64792 \r\n----------------------------------------------------------\r\n#========================================================#\r\n#|         OpenMM energy components via ParmEd          |#\r\n#========================================================#\r\nHarmonicBondForce         6.50352751114e-22 \r\nHarmonicAngleForce        1405.73542001 \r\nPeriodicTorsionForce      236.932662914 \r\nRBTorsionForce            428.055059856 \r\nCustomTorsionForce        33.201541613 \r\nNonbondedForce            -17427.3113967 \r\nCMMotionRemover           0.0 \r\nPotential                 -15323.3867123 \r\n----------------------------------------------------------\r\n#========================================================#\r\n#|               AMBER energy components                |#\r\n#========================================================#\r\nBOND                      0.0 \r\nANGLE                     1405.7352992 \r\nDIHED                     236.9328072 \r\n1-4 NB                    716.4510056 \r\n1-4 EEL                   5181.886092 \r\nVDWAALS                   3195.9375216 \r\nEELEC                     -26522.0835384 \r\nVIRIAL                    871.8933 \r\nEPTOT                     -15785.1403944 \r\n----------------------------------------------------------\r\n```"}}