{"action":"closed","issue":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/1586","repository_url":"https://api.github.com/repos/pandegroup/openmm","labels_url":"https://api.github.com/repos/pandegroup/openmm/issues/1586/labels{/name}","comments_url":"https://api.github.com/repos/pandegroup/openmm/issues/1586/comments","events_url":"https://api.github.com/repos/pandegroup/openmm/issues/1586/events","html_url":"https://github.com/pandegroup/openmm/issues/1586","id":176099538,"number":1586,"title":"Particle coordinate is nan error related to GB forces.","user":{"login":"bas-rustenburg","id":3977731,"avatar_url":"https://avatars.githubusercontent.com/u/3977731?v=3","gravatar_id":"","url":"https://api.github.com/users/bas-rustenburg","html_url":"https://github.com/bas-rustenburg","followers_url":"https://api.github.com/users/bas-rustenburg/followers","following_url":"https://api.github.com/users/bas-rustenburg/following{/other_user}","gists_url":"https://api.github.com/users/bas-rustenburg/gists{/gist_id}","starred_url":"https://api.github.com/users/bas-rustenburg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bas-rustenburg/subscriptions","organizations_url":"https://api.github.com/users/bas-rustenburg/orgs","repos_url":"https://api.github.com/users/bas-rustenburg/repos","events_url":"https://api.github.com/users/bas-rustenburg/events{/privacy}","received_events_url":"https://api.github.com/users/bas-rustenburg/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-09-09T20:17:01Z","updated_at":"2016-09-22T20:55:44Z","closed_at":"2016-09-22T20:55:44Z","body":"I've been experiencing some issues running implicit solvent simulations. In our particular test case, we observe crashes for a `ACE-TYR-NME` system. They occur often, but it is hard to reproduce the exact moment when it's going to happen. \r\n\r\n@jchodera discovered that the errors disappear when we eliminate `GBSAOBC` Forces from the system. \r\n\r\nHere is the minimal example, which contains the script, and serialized systems with and without GB forces. This is using openmm 7.0.1. I included the conda environment specifications in the zip file.\r\n\r\n[debug.zip](https://github.com/pandegroup/openmm/files/464730/debug.zip)\r\n\r\nWhen we run the script included, we get these errors, which happen in some iteration of the loop.\r\n\r\n```pytb\r\nTraceback (most recent call last):\r\n  File \"minimal.py\", line 26, in <module>\r\n    integrator.step(10)  # MD\r\n  File \"/home/rustenburg/anaconda/envs/gbforces/lib/python2.7/site-packages/simtk/openmm/openmm.py\", line 5330, in step\r\n    return _openmm.CustomIntegrator_step(self, steps)\r\nException: Particle coordinate is nan\r\n```\r\n\r\nIt is hard to reproduce exactly the moment where it fails, but it is bound to happen if we run the loop for a few iterations. It does not occur when we remove GB forces.  We think there could be a numerical issue with the GB forces that is causing this behavior.\r\n\r\n"}}
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