{"action":"created","issue":{"url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/187","repository_url":"https://api.github.com/repos/open-forcefield-group/smarty","labels_url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/187/labels{/name}","comments_url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/187/comments","events_url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/187/events","html_url":"https://github.com/open-forcefield-group/smarty/pull/187","id":190882198,"number":187,"title":"[WIP] Add conversion to AMBER and GROMACS formats","user":{"login":"davidlmobley","id":7132257,"avatar_url":"https://avatars.githubusercontent.com/u/7132257?v=3","gravatar_id":"","url":"https://api.github.com/users/davidlmobley","html_url":"https://github.com/davidlmobley","followers_url":"https://api.github.com/users/davidlmobley/followers","following_url":"https://api.github.com/users/davidlmobley/following{/other_user}","gists_url":"https://api.github.com/users/davidlmobley/gists{/gist_id}","starred_url":"https://api.github.com/users/davidlmobley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidlmobley/subscriptions","organizations_url":"https://api.github.com/users/davidlmobley/orgs","repos_url":"https://api.github.com/users/davidlmobley/repos","events_url":"https://api.github.com/users/davidlmobley/events{/privacy}","received_events_url":"https://api.github.com/users/davidlmobley/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-11-22T01:17:25Z","updated_at":"2016-11-22T21:39:02Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/open-forcefield-group/smarty/pulls/187","html_url":"https://github.com/open-forcefield-group/smarty/pull/187","diff_url":"https://github.com/open-forcefield-group/smarty/pull/187.diff","patch_url":"https://github.com/open-forcefield-group/smarty/pull/187.patch"},"body":"Here I'll add conversion to AMBER and GROMACS formats as per #184 :\r\n- [ ] Convert to AMBER format \r\n- [ ] Convert to GROMACS format\r\n- [ ] Add test validating energies before and after conversion\r\n\r\nSeveral other issues were fixed in the process:\r\n- [x] Extraneous print statement removed\r\n- [x] Better debug info for a nonbonded force exception\r\n- [x] Fix #186 bug with charges\r\n- [x] Fix documentation issue noted in #186 \r\n\r\nOther things to fix as well:\r\n- [ ] Add a test that multiple instances of a particular molecule in a system get correct charges (not just the first molecule) per #186 \r\n"},"comment":{"url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/comments/262373591","html_url":"https://github.com/open-forcefield-group/smarty/pull/187#issuecomment-262373591","issue_url":"https://api.github.com/repos/open-forcefield-group/smarty/issues/187","id":262373591,"user":{"login":"davidlmobley","id":7132257,"avatar_url":"https://avatars.githubusercontent.com/u/7132257?v=3","gravatar_id":"","url":"https://api.github.com/users/davidlmobley","html_url":"https://github.com/davidlmobley","followers_url":"https://api.github.com/users/davidlmobley/followers","following_url":"https://api.github.com/users/davidlmobley/following{/other_user}","gists_url":"https://api.github.com/users/davidlmobley/gists{/gist_id}","starred_url":"https://api.github.com/users/davidlmobley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidlmobley/subscriptions","organizations_url":"https://api.github.com/users/davidlmobley/orgs","repos_url":"https://api.github.com/users/davidlmobley/repos","events_url":"https://api.github.com/users/davidlmobley/events{/privacy}","received_events_url":"https://api.github.com/users/davidlmobley/received_events","type":"User","site_admin":false},"created_at":"2016-11-22T21:39:02Z","updated_at":"2016-11-22T21:39:02Z","body":"Differences in Coulomb constant don't seem to explain it; the difference is far too small. 332.0522 in AMBER, and the most different other code has 332.0637 or so. \r\n\r\nAlso, it's odd that this only occurs here and in none of our prior tests. I wonder if I have some sort of lingering issue with copying charges, where the forces in OpenMM are somehow being applied with slightly different charges than are originally in the molecules or some such. Investigating..."}}
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