{"action":"created","issue":{"url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1165","repository_url":"https://api.github.com/repos/Amber-MD/pytraj","labels_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1165/labels{/name}","comments_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1165/comments","events_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1165/events","html_url":"https://github.com/Amber-MD/pytraj/issues/1165","id":139942295,"number":1165,"title":"rdf question","user":{"login":"jdmadura","id":17444103,"avatar_url":"https://avatars.githubusercontent.com/u/17444103?v=3","gravatar_id":"","url":"https://api.github.com/users/jdmadura","html_url":"https://github.com/jdmadura","followers_url":"https://api.github.com/users/jdmadura/followers","following_url":"https://api.github.com/users/jdmadura/following{/other_user}","gists_url":"https://api.github.com/users/jdmadura/gists{/gist_id}","starred_url":"https://api.github.com/users/jdmadura/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdmadura/subscriptions","organizations_url":"https://api.github.com/users/jdmadura/orgs","repos_url":"https://api.github.com/users/jdmadura/repos","events_url":"https://api.github.com/users/jdmadura/events{/privacy}","received_events_url":"https://api.github.com/users/jdmadura/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-03-10T16:31:44Z","updated_at":"2016-03-10T19:57:01Z","closed_at":null,"body":"When I use the rdf() command to calculate the radial distribution function between a water oxygen and a small molecule atom the shape of the g(r) looks fine; however, the actual values appear to be low.  The water-water rdfs look fine.  The Ipython notebook is attached.  The trajectory file is 33 MB in size.\r\n[pytraj_md.ipynb.zip](https://github.com/Amber-MD/pytraj/files/167562/pytraj_md.ipynb.zip)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/Amber-MD/pytraj/issues/comments/195021756","html_url":"https://github.com/Amber-MD/pytraj/issues/1165#issuecomment-195021756","issue_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1165","id":195021756,"user":{"login":"drroe","id":10144183,"avatar_url":"https://avatars.githubusercontent.com/u/10144183?v=3","gravatar_id":"","url":"https://api.github.com/users/drroe","html_url":"https://github.com/drroe","followers_url":"https://api.github.com/users/drroe/followers","following_url":"https://api.github.com/users/drroe/following{/other_user}","gists_url":"https://api.github.com/users/drroe/gists{/gist_id}","starred_url":"https://api.github.com/users/drroe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drroe/subscriptions","organizations_url":"https://api.github.com/users/drroe/orgs","repos_url":"https://api.github.com/users/drroe/repos","events_url":"https://api.github.com/users/drroe/events{/privacy}","received_events_url":"https://api.github.com/users/drroe/received_events","type":"User","site_admin":false},"created_at":"2016-03-10T19:57:01Z","updated_at":"2016-03-10T19:57:01Z","body":"I just did a test calculation with cpptraj for a simple system (trpzip2 beta hairpin in water) in both orthogonal and truncated octahedal cells. Here is the cpptraj input:\r\n```\r\nrdf out rdf.agr 0.05 8 :WAT@O :WAT@O O_O\r\nrdf out rdf.agr 0.05 8 :WAT@O :WAT@H= O_H nointramol\r\n```\r\nResults for both are below; looks good to me.\r\n![rdf formatted](https://cloud.githubusercontent.com/assets/10144183/13682494/3e29ccfc-e6bf-11e5-9b75-6f8b5b22458f.jpg)\r\n![rdf formatted](https://cloud.githubusercontent.com/assets/10144183/13682511/503bc24c-e6bf-11e5-9c21-2de3cfad21a8.jpg)\r\n@jdmadura out of curiosity if you repeat the calculation with just cpptraj do you still obtain the same results? This way we can decide if it's an underlying cpptraj issue or not."}}