{"action":"created","issue":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/1855","repository_url":"https://api.github.com/repos/pandegroup/openmm","labels_url":"https://api.github.com/repos/pandegroup/openmm/issues/1855/labels{/name}","comments_url":"https://api.github.com/repos/pandegroup/openmm/issues/1855/comments","events_url":"https://api.github.com/repos/pandegroup/openmm/issues/1855/events","html_url":"https://github.com/pandegroup/openmm/issues/1855","id":240717776,"number":1855,"title":"Additional virtual site types","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars2.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":19,"created_at":"2017-07-05T17:12:16Z","updated_at":"2017-07-11T03:54:48Z","closed_at":null,"body":"As part of the ongoing evolution of the [SMIRNOFF SMARTS-based forcefield specification scheme](https://github.com/open-forcefield-group/smirnoff/blob/master/The-SMIRNOFF-force-field-format.md), there is a growing desire to support off-atom charge sites to represent lone pairs or sigma holes. While OpenMM already has a variety of supported virtual site geometries, it appears we are missing a few key geometries that would be necessary to support lone pairs and sigma holes.\r\n\r\nThe current proposal adds XML syntax that looks like this:\r\n```XML\r\n<!-- sigma hole for halogens: \"distance\" denotes distance along the 2->1 bond vector -->\r\n<VirtualSite type=\"BondCharge\" smirks=\"[Cl:1]-[C:2]\" distance=\"0.30\"/>\r\n<!-- monovalent lone pairs: carbonyl -->\r\n<!-- inPlaneAngle is angle charge site (X) makes with 1 and 2, i.e. X-1-2 -->\r\n<!-- outOfPlaneAngle is angle charge site (X) makes out of the plane of 2-1-3 measured from 1 -->\r\n<VirtualSite type=\"MonovalentLonePair\" smirks=\"[O:1]=[C:2]-[*:3]\" distance=\"0.30\" outOfPlaneAngle=\"0\" inPlaneAngle=\"120\"/>\r\n<!-- divalent lone pair: pyrimidine -->\r\n<!-- single charge site lies in plane, bisecting the angle left by taking 360 degrees minus angle(2,1,3) -->\r\n<VirtualSite type=\"DivalentLonePair\" smirks=\"[*:2]~[#7X2:1]~[*:3]\" distance=\"0.30\"/>\r\n<!-- trivalent nitrogen lone pair -->\r\n<!-- charge sites lie above and below the nitrogen at specified distances from the nitrogen, along the vector perpendicular to the plane of (2,3,4) that passes through the nitrogen. If the nitrogen is co-planar with the connected atom, charge sites are simply above and below the plane-->\r\n<!-- Positive and negative values refer to above or below the nitrogen as measured relative to the plane of (2,3,4), i.e. below the nitrogen means nearer the 2,3,4 plane unless they are co-planar -->\r\n<VirtualSite type=\"TrivalentLonePair\" smirks=\"[*:2]~[#7X3:1](~[*:4])~[*:3]\" distance=\"0.30\"/>\r\n<VirtualSite type=\"TrivalentLonePair\" smirks=\"[*:2]~[#7X3:1](~[*:4])~[*:3]\" distance=\"-0.30\"/>\r\n```\r\nAs I see it, this would require a few additional types of `VirtualSite` subclasses in addition to [those already implemented](http://docs.openmm.org/7.1.0/userguide/theory.html#virtual-sites). For example, for \"BondCharge\" above, `TwoParticleAverageSite` won't work because we need to specify the displacement distance from atom 1 along the bond vector, rather than simply specify the fractional bond distance---this is due to the quantum chemical effects driving where this charge center is best placed. The other `type`s above have similar differences from existing virtual site types.\r\n\r\nDoes it sound practical for these additional virtual site types to be defined?\r\n\r\nWe're currently discussing this in https://github.com/open-forcefield-group/openforcefield/issues/41 (original thread [here](https://github.com/open-forcefield-group/smarty/issues/132)) if more detail is needed."},"comment":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/comments/314315796","html_url":"https://github.com/pandegroup/openmm/issues/1855#issuecomment-314315796","issue_url":"https://api.github.com/repos/pandegroup/openmm/issues/1855","id":314315796,"user":{"login":"davidlmobley","id":7132257,"avatar_url":"https://avatars3.githubusercontent.com/u/7132257?v=3","gravatar_id":"","url":"https://api.github.com/users/davidlmobley","html_url":"https://github.com/davidlmobley","followers_url":"https://api.github.com/users/davidlmobley/followers","following_url":"https://api.github.com/users/davidlmobley/following{/other_user}","gists_url":"https://api.github.com/users/davidlmobley/gists{/gist_id}","starred_url":"https://api.github.com/users/davidlmobley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidlmobley/subscriptions","organizations_url":"https://api.github.com/users/davidlmobley/orgs","repos_url":"https://api.github.com/users/davidlmobley/repos","events_url":"https://api.github.com/users/davidlmobley/events{/privacy}","received_events_url":"https://api.github.com/users/davidlmobley/received_events","type":"User","site_admin":false},"created_at":"2017-07-11T03:54:48Z","updated_at":"2017-07-11T03:54:48Z","body":"I am following up with @cbayly13 on the `DivalentLonePair` case, though I believe he's out of town this week so he may not be able to get back to us for a bit. I'm investigating the others now and hope to respond shortly."}}
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