{"action":"created","issue":{"url":"https://api.github.com/repos/salilab/pmi/issues/165","labels_url":"https://api.github.com/repos/salilab/pmi/issues/165/labels{/name}","comments_url":"https://api.github.com/repos/salilab/pmi/issues/165/comments","events_url":"https://api.github.com/repos/salilab/pmi/issues/165/events","html_url":"https://github.com/salilab/pmi/issues/165","id":130469430,"number":165,"title":"Shuffle sucks - sample instead?","user":{"login":"cgreenberg","id":1170706,"avatar_url":"https://avatars.githubusercontent.com/u/1170706?v=3","gravatar_id":"","url":"https://api.github.com/users/cgreenberg","html_url":"https://github.com/cgreenberg","followers_url":"https://api.github.com/users/cgreenberg/followers","following_url":"https://api.github.com/users/cgreenberg/following{/other_user}","gists_url":"https://api.github.com/users/cgreenberg/gists{/gist_id}","starred_url":"https://api.github.com/users/cgreenberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cgreenberg/subscriptions","organizations_url":"https://api.github.com/users/cgreenberg/orgs","repos_url":"https://api.github.com/users/cgreenberg/repos","events_url":"https://api.github.com/users/cgreenberg/events{/privacy}","received_events_url":"https://api.github.com/users/cgreenberg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-01T20:09:58Z","updated_at":"2016-02-01T20:58:59Z","closed_at":null,"body":"It won't work unless the rigid parts are already separated. Better idea would be to just simulate for a while  with only stereochemistry as the restraint. An easy solution would be to add a new macro (or add an option to replica exchange) to just disable all restraints but EVSphere and just run monte carlo for a while."},"comment":{"url":"https://api.github.com/repos/salilab/pmi/issues/comments/178186418","html_url":"https://github.com/salilab/pmi/issues/165#issuecomment-178186418","issue_url":"https://api.github.com/repos/salilab/pmi/issues/165","id":178186418,"user":{"login":"Pellarin","id":2477712,"avatar_url":"https://avatars.githubusercontent.com/u/2477712?v=3","gravatar_id":"","url":"https://api.github.com/users/Pellarin","html_url":"https://github.com/Pellarin","followers_url":"https://api.github.com/users/Pellarin/followers","following_url":"https://api.github.com/users/Pellarin/following{/other_user}","gists_url":"https://api.github.com/users/Pellarin/gists{/gist_id}","starred_url":"https://api.github.com/users/Pellarin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Pellarin/subscriptions","organizations_url":"https://api.github.com/users/Pellarin/orgs","repos_url":"https://api.github.com/users/Pellarin/repos","events_url":"https://api.github.com/users/Pellarin/events{/privacy}","received_events_url":"https://api.github.com/users/Pellarin/received_events","type":"User","site_admin":false},"created_at":"2016-02-01T20:58:59Z","updated_at":"2016-02-01T20:58:59Z","body":"I disagree. Monte Carlo perturbation cannot guarantee a totally random initial conformation, where you've lost memory of the initial conformation. In other words, nobody can tell you how many MC steps are needed. We need to randomize the coordinates in the way we are currently doing, randomly displacing and rotating rigid bodies and beads."}}