{"action":"opened","issue":{"url":"https://api.github.com/repos/philipwfowler/alchembed-tutorial/issues/1","repository_url":"https://api.github.com/repos/philipwfowler/alchembed-tutorial","labels_url":"https://api.github.com/repos/philipwfowler/alchembed-tutorial/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/philipwfowler/alchembed-tutorial/issues/1/comments","events_url":"https://api.github.com/repos/philipwfowler/alchembed-tutorial/issues/1/events","html_url":"https://github.com/philipwfowler/alchembed-tutorial/issues/1","id":131046496,"number":1,"title":"Protein deformation after the alchemical simulation","user":{"login":"yiannisgaldadas","id":17047673,"avatar_url":"https://avatars.githubusercontent.com/u/17047673?v=3","gravatar_id":"","url":"https://api.github.com/users/yiannisgaldadas","html_url":"https://github.com/yiannisgaldadas","followers_url":"https://api.github.com/users/yiannisgaldadas/followers","following_url":"https://api.github.com/users/yiannisgaldadas/following{/other_user}","gists_url":"https://api.github.com/users/yiannisgaldadas/gists{/gist_id}","starred_url":"https://api.github.com/users/yiannisgaldadas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yiannisgaldadas/subscriptions","organizations_url":"https://api.github.com/users/yiannisgaldadas/orgs","repos_url":"https://api.github.com/users/yiannisgaldadas/repos","events_url":"https://api.github.com/users/yiannisgaldadas/events{/privacy}","received_events_url":"https://api.github.com/users/yiannisgaldadas/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-02-03T14:45:43Z","updated_at":"2016-02-03T14:45:43Z","closed_at":null,"body":"The following report refers to the difficulties that I had when I tried to embed a GPCR to a mixed DMPC/cholesterol lipid bilayer. Specifically, parts of the protein were seriously deformed after applying the alchembed approach. The process that I followed for the embedding is as follows.\r\n\r\nFirst, I placed the GPCR to the desired position inside the solvated and pre-equilibrated bilayer using the editconf tool of GROMACS 5.0.7. Then I removed any lipid and water that was less than 5 Å away from the the centre of mass of the protein using the same tool and an appropriate index file. After visual inspection of the resulting structure with VMD, I proceeded to delete some additional lipids that seriously overlapped with the protein, i. e. the ones that their tails were seriously penetrating the alpha helices of the receptor. When I obtained a satisfactory initial structure, I proceeded with the protocol that is described in the alchembed tutorial, i.e. energy minimization follwed by the alchemical simulation. First, I used the exact same parameters that are described in the .mdp file of the tutorial. Nonetheless, the resulting structure had some serious deformations both in the transmembrane domain and in some extracelluar loops. The problem was fixed though when I decreased dt from 0.001 fs to 0.0005 fs.\r\n\r\nIt should be noted that the packing of the lipids around the protein was better (tighter) using the alchembed approach, compared to the one that I got when I embedded the protein using the g_membed tool of GROMACS 4.5.5. More over, the resulting structure had a few more lipids and water molecules, as I did not have to delete all those molecules that g_membed deletes.\""}}