{"action":"created","issue":{"url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/11","repository_url":"https://api.github.com/repos/bio-phys/PyDHAMed","labels_url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/11/comments","events_url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/11/events","html_url":"https://github.com/bio-phys/PyDHAMed/issues/11","id":299064091,"number":11,"title":"Bias potential matrix","user":{"login":"andt88","id":36545428,"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":48,"created_at":"2018-02-21T17:42:24Z","updated_at":"2018-05-19T08:29:59Z","closed_at":null,"author_association":"NONE","body":"Hi, \r\nI wanted to make sure that I understand the definition of the bias potential matrix correctly.\r\nAssuming an umbrella sampling experiment with 4 windows A, B, C, D and 3 states 0, 1, 2. The restraining potential defined as k*(x-x0)^2. Should the cell A0 contain the following?\r\nx=median value of bin 0, \r\nx0=target value of window A\r\n"},"comment":{"url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/comments/390389448","html_url":"https://github.com/bio-phys/PyDHAMed/issues/11#issuecomment-390389448","issue_url":"https://api.github.com/repos/bio-phys/PyDHAMed/issues/11","id":390389448,"user":{"login":"lukas-stelzl","id":20243278,"avatar_url":"https://avatars1.githubusercontent.com/u/20243278?v=4","gravatar_id":"","url":"https://api.github.com/users/lukas-stelzl","html_url":"https://github.com/lukas-stelzl","followers_url":"https://api.github.com/users/lukas-stelzl/followers","following_url":"https://api.github.com/users/lukas-stelzl/following{/other_user}","gists_url":"https://api.github.com/users/lukas-stelzl/gists{/gist_id}","starred_url":"https://api.github.com/users/lukas-stelzl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lukas-stelzl/subscriptions","organizations_url":"https://api.github.com/users/lukas-stelzl/orgs","repos_url":"https://api.github.com/users/lukas-stelzl/repos","events_url":"https://api.github.com/users/lukas-stelzl/events{/privacy}","received_events_url":"https://api.github.com/users/lukas-stelzl/received_events","type":"User","site_admin":false},"created_at":"2018-05-19T08:29:58Z","updated_at":"2018-05-19T08:29:58Z","author_association":"MEMBER","body":"Hi, I'm sorry for the slow response. pyDHAMed does not include such functions yet, but I'm working on including them.\r\n\r\n1) I will have quick look at calculating the covariance matrix from F next week #12. \r\n2) Calculating kinetics from e.g., umbrella sampling is tricky. I will think about a strategy that might work for you and others and what functions should be included in the package.  #13. "}}
{"actor":{"display_login":"lukas-stelzl"}}