{"action":"created","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/766","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/766/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/766/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/766/events","html_url":"https://github.com/Acellera/htmd/issues/766","id":356258666,"node_id":"MDU6SXNzdWUzNTYyNTg2NjY=","number":766,"title":"HTMD get's stuck on metrics projection","user":{"login":"andt88","id":36545428,"node_id":"MDQ6VXNlcjM2NTQ1NDI4","avatar_url":"https://avatars2.githubusercontent.com/u/36545428?v=4","gravatar_id":"","url":"https://api.github.com/users/andt88","html_url":"https://github.com/andt88","followers_url":"https://api.github.com/users/andt88/followers","following_url":"https://api.github.com/users/andt88/following{/other_user}","gists_url":"https://api.github.com/users/andt88/gists{/gist_id}","starred_url":"https://api.github.com/users/andt88/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andt88/subscriptions","organizations_url":"https://api.github.com/users/andt88/orgs","repos_url":"https://api.github.com/users/andt88/repos","events_url":"https://api.github.com/users/andt88/events{/privacy}","received_events_url":"https://api.github.com/users/andt88/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-02T07:06:42Z","updated_at":"2018-09-02T07:56:07Z","closed_at":null,"author_association":"NONE","body":"When following the ligand binding tutorial on my own data set, the program seems to get stuck after running\r\n\r\n```\r\nmetr = Metric(sims)\r\nmetr.set(MetricDistance('protein and name CA', 'resname MOL and noh', metric='contacts'))\r\ndata = metr.project()\r\n```\r\nThe machine slows down and becomes impossible to work with.\r\n\r\nThe output I get:\r\n```\r\n2018-09-02 09:01:39,200 - htmd.molecule.readers - WARNING - Atoms with names \"HG11\" \"HG12\" \"HG13\" \"HG21\" \"HG22\" \"HG23\" were guessed as element H but could also be Hg (mercury). If this is a case, you can correct them with mol.set('element', 'Hg', sel='name \"HG11\" \"HG12\" \"HG13\" \"HG21\" \"HG22\" \"HG23\"')\r\n2018-09-02 09:01:39,200 - htmd.molecule.readers - WARNING - Atoms with names \"HE21\" \"HE22\" were guessed as element H but could also be He (helium). If this is a case, you can correct them with mol.set('element', 'He', sel='name \"HE21\" \"HE22\"')\r\n/home/local/andtos-loc/anaconda3/lib/python3.5/site-packages/pandas/core/frame.py:6211: FutureWarning: Sorting because non-concatenation axis is not aligned. A future version\r\nof pandas will change to not sort by default.\r\n\r\nTo accept the future behavior, pass 'sort=False'.\r\n\r\nTo retain the current behavior and silence the warning, pass 'sort=True'.\r\n\r\n  sort=sort)\r\nProjecting trajectories: 100%|              | 8/8 [00:00<00:00, 31.13it/s]\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/Acellera/htmd/issues/comments/417912142","html_url":"https://github.com/Acellera/htmd/issues/766#issuecomment-417912142","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/766","id":417912142,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNzkxMjE0Mg==","user":{"login":"stefdoerr","id":7935362,"node_id":"MDQ6VXNlcjc5MzUzNjI=","avatar_url":"https://avatars3.githubusercontent.com/u/7935362?v=4","gravatar_id":"","url":"https://api.github.com/users/stefdoerr","html_url":"https://github.com/stefdoerr","followers_url":"https://api.github.com/users/stefdoerr/followers","following_url":"https://api.github.com/users/stefdoerr/following{/other_user}","gists_url":"https://api.github.com/users/stefdoerr/gists{/gist_id}","starred_url":"https://api.github.com/users/stefdoerr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefdoerr/subscriptions","organizations_url":"https://api.github.com/users/stefdoerr/orgs","repos_url":"https://api.github.com/users/stefdoerr/repos","events_url":"https://api.github.com/users/stefdoerr/events{/privacy}","received_events_url":"https://api.github.com/users/stefdoerr/received_events","type":"User","site_admin":false},"created_at":"2018-09-02T07:56:07Z","updated_at":"2018-09-02T07:56:07Z","author_association":"CONTRIBUTOR","body":"You are filling up your RAM and going into swap. Reduce the number of CPUs\r\n\r\n```python\r\nfrom htmd.config import config\r\nconfig(ncpu=1)\r\n```"}}
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