{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3","repository_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling","labels_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3/comments","events_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3/events","html_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3","id":169583519,"number":3,"title":"Set up host-guest ligand unbinding TIS","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2016-08-05T11:02:36Z","updated_at":"2016-08-05T11:27:39Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/pulls/3","html_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3","diff_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3.diff","patch_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3.patch"},"body":"Here's a clean new PR so that you can comment line by line, @jhprinz @dwhswenson \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/comments/237827504","html_url":"https://github.com/choderalab/ligand-binding-pathsampling/pull/3#issuecomment-237827504","issue_url":"https://api.github.com/repos/choderalab/ligand-binding-pathsampling/issues/3","id":237827504,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"created_at":"2016-08-05T11:27:39Z","updated_at":"2016-08-05T11:27:39Z","body":"Definite progress here:\r\n```\r\nCreating interface list...\r\nDefine initial core...\r\nGenerate initial trajectory...\r\nbound  :    2.83 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +\r\nunbound:    2.83 - - - - - - - - - - - - + + + + + + + + + + + + + + + + + +\r\nThe initial configuration is in state unbound\r\nGenerate intercore trajectories...\r\n[   1]    2  bound   <   33 > bound     still missing states unbound\r\n[   2]    3  bound   <   29 > bound     still missing states unbound\r\n[   3]    4  bound   <   24 > bound     still missing states unbound\r\n[   4]    5  bound   <   23 > bound     still missing states unbound\r\n[   5]    6  bound   <   19 > bound     still missing states unbound\r\n[   6]    7  bound   <   20 > bound     still missing states unbound\r\n[   7]    8  bound   <   20 > bound     still missing states unbound\r\n[   8]    9  bound   <   17 > bound     still missing states unbound\r\n[   9]   10  bound   <   20 > bound     still missing states unbound\r\n[  10]   11  bound   <   22 > bound     still missing states unbound\r\n[  11]   12  bound   <   18 > bound     still missing states unbound\r\n[  12]   13  bound   <   23 > bound     still missing states unbound\r\n[  13]   14  bound   <   61 > bound     still missing states unbound\r\n[  14]   15  bound   <   11 > bound     still missing states unbound\r\n[  15]   16  bound   <   13 > bound     still missing states unbound\r\n[  16]   17  bound   <   12 > bound     still missing states unbound\r\n[  17]   18  bound   <   10 > bound     still missing states unbound\r\n[  18]   19  bound   <   12 > bound     still missing states unbound\r\n[  19]   20  bound   <   24 > bound     still missing states unbound\r\n[  20]   21  bound   <   21 > bound     still missing states unbound\r\n[  21]   22  bound   <   24 > bound     still missing states unbound\r\n[  22]   23  bound   <   28 > bound     still missing states unbound\r\n[  23]   24  bound   <   40 > bound     still missing states unbound\r\n[  24]   25  bound   <   29 > bound     still missing states unbound\r\n[  25]   26  bound   <   19 > bound     still missing states unbound\r\n[  26]   27  bound   <   21 > bound     still missing states unbound\r\n[  27]   28  bound   <   14 > bound     still missing states unbound\r\n[  28]   29  bound   <    3 > bound     still missing states unbound\r\n[  29]   30  bound   <    3 > bound     still missing states unbound\r\n[  30]   31  bound   <    2 > bound     still missing states unbound\r\n[  31]   32  bound   <    3 > bound     still missing states unbound\r\n[  32]   33  bound   <    3 > bound     still missing states unbound\r\n[  33]   34  bound   <    2 > bound     still missing states unbound\r\n[  34]   35  bound   <    2 > bound     still missing states unbound\r\n[  35]   36  bound   <    2 > bound     still missing states unbound\r\n[  36]   37  bound   <    2 > bound     still missing states unbound\r\n[  37]   38  bound   <    2 > bound     still missing states unbound\r\n[  38]   39  bound   <    1 > bound     still missing states unbound\r\n[  39]   40  bound   <    1 > bound     still missing states unbound\r\n[  40]   41  bound   <    1 > bound     still missing states unbound\r\n[  41]   42  bound   <    1 > bound     still missing states unbound\r\n[  42]   43  bound   <    1 > bound     still missing states unbound\r\n[  43]   44  bound   <    1 > bound     still missing states unbound\r\n[  44]   45  bound   <    1 > bound     still missing states unbound\r\n[  45]   46  bound   <    1 > bound     still missing states unbound\r\n[  46]   47  bound   <    1 > bound     still missing states unbound\r\n[  47]   48  bound   <    1 > bound     still missing states unbound\r\n[  48]   49  bound   <    1 > bound     still missing states unbound\r\n[  49]   50  bound   <    1 > bound     still missing states unbound\r\n[  50]   51  bound   <    1 > bound     still missing states unbound\r\n[  51]   52  bound   <    1 > bound     still missing states unbound\r\n[  52]   53  bound   <    1 > bound     still missing states unbound\r\n[  53]   54  bound   <    3 > bound     still missing states unbound\r\n[  54]   55  bound   <   13 > bound     still missing states unbound\r\nTraceback (most recent call last):\r\n  File \"setup-ops.py\", line 246, in <module>\r\n    tt = engine_hot.generate_forward(tt[-1].reversed, core2core)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/engines/dynamics_engine.py\", line 284, in generate_forward\r\n    return self.generate(snapshot, ensemble.can_append, direction=+1)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/engines/dynamics_engine.py\", line 361, in generate\r\n    snapshot = self.generate_next_frame()\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/engines/openmm/engine.py\", line 257, in generate_next_frame\r\n    self.simulation.step(self.n_steps_per_frame)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/simtk/openmm/app/simulation.py\", line 132, in step\r\n    self._simulate(endStep=self.currentStep+steps)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/simtk/openmm/app/simulation.py\", line 198, in _simulate\r\n    self.integrator.step(stepsToGo)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/simtk/openmm/openmm.py\", line 13564, in step\r\n    return _openmm.LangevinIntegrator_step(self, steps)\r\nException: Particle coordinate is nan\r\n```\r\nThis is presumably a `nan` induced by the high-temperature simulation, right?"}}
{"actor":{"display_login":"jchodera"}}