{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/yank-benchmark/issues/1","repository_url":"https://api.github.com/repos/choderalab/yank-benchmark","labels_url":"https://api.github.com/repos/choderalab/yank-benchmark/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/yank-benchmark/issues/1/comments","events_url":"https://api.github.com/repos/choderalab/yank-benchmark/issues/1/events","html_url":"https://github.com/choderalab/yank-benchmark/pull/1","id":248608350,"number":1,"title":"Add initial cyclodextrin files","user":{"login":"andrrizzi","id":1682142,"avatar_url":"https://avatars3.githubusercontent.com/u/1682142?v=4","gravatar_id":"","url":"https://api.github.com/users/andrrizzi","html_url":"https://github.com/andrrizzi","followers_url":"https://api.github.com/users/andrrizzi/followers","following_url":"https://api.github.com/users/andrrizzi/following{/other_user}","gists_url":"https://api.github.com/users/andrrizzi/gists{/gist_id}","starred_url":"https://api.github.com/users/andrrizzi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrrizzi/subscriptions","organizations_url":"https://api.github.com/users/andrrizzi/orgs","repos_url":"https://api.github.com/users/andrrizzi/repos","events_url":"https://api.github.com/users/andrrizzi/events{/privacy}","received_events_url":"https://api.github.com/users/andrrizzi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2017-08-08T05:57:21Z","updated_at":"2017-08-08T20:41:44Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/yank-benchmark/pulls/1","html_url":"https://github.com/choderalab/yank-benchmark/pull/1","diff_url":"https://github.com/choderalab/yank-benchmark/pull/1.diff","patch_url":"https://github.com/choderalab/yank-benchmark/pull/1.patch"},"body":"Here are the initial host-guest files.\r\n\r\nNote that this works only with the dev YANK currently in branch `solvent-parameters`.\r\n\r\nCould you take a look at the `cyclodextring.yaml` script and see if there's something that we should change in the protocol? In particular:\r\n1. Which atom should we use to compute the centroids to restrain? For now, I went with the carbon atoms of the ligand and the receptor.\r\n2. Should we use HMR? Any particular time step?\r\n3. I've parametrized everything with AM1-BCC/GAFF (the host as well) rather than using the original RESP charges in the `mol2` files because in Niel Henriksen and Michael Gilson's paper it seems to have given the best statistics overall for binding free energies.\r\n3. The script is configured to assign OpenEye AM1-BCC charges to guests and antechamber bcc charges to hosts. This is because OpenEye on the host gave me this `omega` error:\r\n```\r\nWarning: force field setup failed due to missing parameters for molecule [dodecaholmiooxy-pentakis(holmiooxymethyl)-BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2},BLAH$l^{2}-dodecaosmaheptacyclo[BLAH]dotetracontanyl]methoxyholmium\r\n```\r\n\r\n@davidlmobley this script should give you a good starting point to setup your calculations. Tweak the script as needed. It's still untested (I'll run 5-10 iterations of all the combinations in the next couple of days), but the setup stage should work on the YANK version I mentioned at the top. Note that the online analysis (`options.online_analysis_target_error`) and the automatic selection of the alchemical path (`protocols.binding-auto.complex.alchemical_path=auto`) are very recent features, and we haven't run simulations with these activated yet, so you may want to just specify a finite number of iterations (`options.number_of_iterations`) and your own alchemical path for now.\r\n\r\nIf you just want to create and inspect the system files, run this\r\n```python\r\nfrom yank.experiment import ExperimentBuilder\r\n\r\nexp_builder = ExperimentBuilder('cyclodextrin.yaml')\r\nexp_builder.setup_experiments()\r\n```"},"comment":{"url":"https://api.github.com/repos/choderalab/yank-benchmark/issues/comments/321075827","html_url":"https://github.com/choderalab/yank-benchmark/pull/1#issuecomment-321075827","issue_url":"https://api.github.com/repos/choderalab/yank-benchmark/issues/1","id":321075827,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars1.githubusercontent.com/u/3656088?v=4","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":"2017-08-08T20:41:43Z","updated_at":"2017-08-08T20:41:43Z","body":"> I'm going to be tied up for the next few hours, so I can just comment really quickly that, since the purpose here is to benchmark agreement (and efficiency) versus existing gold standard data from Niel, and NOT so much to compare against experiment, then you would presumably want to run with exactly the same charges he is using rather than reassigning charges.\r\n\r\n@davidlmobley: I think we are once again running into a problem with terminology.\r\n\r\nI want to be very clear so that there is no potential for confusing the different goals of (1) validation (reproducing the results of existing codes for the exact same parameters), (2) performance (comparing the time required to reach a given error threshold for a given set of parameters), and (3) accuracy (assessing how accurately experimental data is reproduced for a given protocol).\r\n\r\nThe goals of our YANK paper include (1) validation and (3) accuracy, but not (2) benchmarking.\r\n\r\nOn the other hand, your work on comparison of restraints methods focuses on (1) validation and (2) benchmarking, but not (3) accuracy.\r\n\r\nOur primary concern for *this* PR, in the `yank-benchmark` repository (which we should maybe call `yank-accuracy` so as to eliminate any potential for confusion), is to evaluate (3) accuracy."}}
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