{"action":"created","issue":{"url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1166","repository_url":"https://api.github.com/repos/Amber-MD/pytraj","labels_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1166/labels{/name}","comments_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1166/comments","events_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1166/events","html_url":"https://github.com/Amber-MD/pytraj/issues/1166","id":139943010,"number":1166,"title":"Error in calculating distances after an RMSD calculation","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":4,"created_at":"2016-03-10T16:34:11Z","updated_at":"2016-03-11T01:35:17Z","closed_at":null,"body":"When using the distance(traj,...) command after performing and rmsd(traj,...) calculation the distances are not calculated correctly.  If one re-reads the trajectory or performs the distance calculation first then the distances are calculated correctly."},"comment":{"url":"https://api.github.com/repos/Amber-MD/pytraj/issues/comments/195135737","html_url":"https://github.com/Amber-MD/pytraj/issues/1166#issuecomment-195135737","issue_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1166","id":195135737,"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},"created_at":"2016-03-11T01:35:16Z","updated_at":"2016-03-11T01:35:16Z","body":"Here are the requested files.  It appears that it is not the call to rmsd() but the call to calc_atomicfluct() that is the culprit. See the attached files.\r\n[test.zip](https://github.com/Amber-MD/pytraj/files/168326/test.zip)\r\n"}}