{"action":"created","issue":{"url":"https://api.github.com/repos/NMRLipids/lipid_ionINTERACTION/issues/8","labels_url":"https://api.github.com/repos/NMRLipids/lipid_ionINTERACTION/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/NMRLipids/lipid_ionINTERACTION/issues/8/comments","events_url":"https://api.github.com/repos/NMRLipids/lipid_ionINTERACTION/issues/8/events","html_url":"https://github.com/NMRLipids/lipid_ionINTERACTION/issues/8","id":118829893,"number":8,"title":"Ulmschneider results for POPC without ions","user":{"login":"ohsOllila","id":7114769,"avatar_url":"https://avatars.githubusercontent.com/u/7114769?v=3","gravatar_id":"","url":"https://api.github.com/users/ohsOllila","html_url":"https://github.com/ohsOllila","followers_url":"https://api.github.com/users/ohsOllila/followers","following_url":"https://api.github.com/users/ohsOllila/following{/other_user}","gists_url":"https://api.github.com/users/ohsOllila/gists{/gist_id}","starred_url":"https://api.github.com/users/ohsOllila/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ohsOllila/subscriptions","organizations_url":"https://api.github.com/users/ohsOllila/orgs","repos_url":"https://api.github.com/users/ohsOllila/repos","events_url":"https://api.github.com/users/ohsOllila/events{/privacy}","received_events_url":"https://api.github.com/users/ohsOllila/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-11-25T12:48:07Z","updated_at":"2015-11-26T09:26:26Z","closed_at":null,"body":"I have calculated the order parameters from two different trajectories ran with Ulmscneider model and the results are essentially different.\r\n\r\nThe results from this trajectory:\r\nhttp://dx.doi.org/10.5281/zenodo.13392\r\nare here:\r\nhttps://github.com/NMRLipids/lipid_ionINTERACTION/blob/master/Data/POPC/NaCl/ULM/0na/OrderParametersMATTI.dat\r\nand copypasted here:\r\n-0.0676466 0.00295541\r\n-0.0644059 0.00294201\r\n0.0287083 0.00415642\r\n0.0585144 0.00541744\r\n-0.316206 0.00424214\r\n-0.301216 0.00679239\r\n-0.29812 0.00717626\r\n-0.282629 0.00473567\r\n0.18337 0.011728\r\nThese are close to what was reported in the NMRlipids I project.\r\n\r\nThe results from this trajectory:\r\nhttp://dx.doi.org/10.5281/zenodo.30904\r\nare here:\r\nhttps://github.com/NMRLipids/lipid_ionINTERACTION/blob/master/Data/POPC/NaCl/ULM/0na/OrderParameters.dat\r\nand copypasted here:\r\n-0.0666512 0.00282814\r\n-0.0569859 0.00328485\r\n0.0395524 0.00475013\r\n0.0489784 0.00486469\r\n-0.226971 0.0134899\r\n-0.21175 0.0104782\r\n-0.224464 0.00942215\r\n-0.249064 0.00435139\r\n-0.0408404 0.00670562\r\nThese are closer to the experimental values.\r\n\r\nThe differences in alpha and beta are in reasonable range but difference in glycerol backbone are significant.\r\n\r\nI have added these results in the ion manuscript since the alpha and beta are in focus here. However, we should find out the origin in the difference.\r\n\r\nPotential reasons I have in mind:\r\n- Mistake in *itp files\r\n- Gromacs version differences. However, in the latter data set the difference between verlet and group scheme was tested and no difference found, see https://github.com/NMRLipids/lipid_ionINTERACTION/tree/master/Data/POPC/NaCl/ULM/0na\r\n- Difference in initial structure, in the first one is from Lipidbook, the second from CHARMM GUI."},"comment":{"url":"https://api.github.com/repos/NMRLipids/lipid_ionINTERACTION/issues/comments/159856647","html_url":"https://github.com/NMRLipids/lipid_ionINTERACTION/issues/8#issuecomment-159856647","issue_url":"https://api.github.com/repos/NMRLipids/lipid_ionINTERACTION/issues/8","id":159856647,"user":{"login":"ohsOllila","id":7114769,"avatar_url":"https://avatars.githubusercontent.com/u/7114769?v=3","gravatar_id":"","url":"https://api.github.com/users/ohsOllila","html_url":"https://github.com/ohsOllila","followers_url":"https://api.github.com/users/ohsOllila/followers","following_url":"https://api.github.com/users/ohsOllila/following{/other_user}","gists_url":"https://api.github.com/users/ohsOllila/gists{/gist_id}","starred_url":"https://api.github.com/users/ohsOllila/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ohsOllila/subscriptions","organizations_url":"https://api.github.com/users/ohsOllila/orgs","repos_url":"https://api.github.com/users/ohsOllila/repos","events_url":"https://api.github.com/users/ohsOllila/events{/privacy}","received_events_url":"https://api.github.com/users/ohsOllila/received_events","type":"User","site_admin":false},"created_at":"2015-11-26T09:26:26Z","updated_at":"2015-11-26T09:26:26Z","body":"I calculated some dihedral angle distribution from both simulation trajectories. There is significant difference in the O-g_3-g_2-g_1 dihedral:\r\n![mattimykhailocomp](https://cloud.githubusercontent.com/assets/7114769/11419453/102d860e-9430-11e5-83fe-f4b091823f89.png)\r\n\r\nThis is most likely the reason for this. If there is no difference in *itp this probably originates from the initial structures. I did check the distribution in the initial structure by Matti and the distribution was similar. If Mykhailo would push the initial structure I could check that one as well. \r\n\r\nThe scripts using the mapping files to calculate dihedrals are *sh files in this commit: https://github.com/NMRLipids/lipid_ionINTERACTION/commit/743e440292bb56390b4f1dde293cd78b787979b7\r\n"}}