{"action":"opened","issue":{"url":"https://api.github.com/repos/michellab/Sire/issues/82","labels_url":"https://api.github.com/repos/michellab/Sire/issues/82/labels{/name}","comments_url":"https://api.github.com/repos/michellab/Sire/issues/82/comments","events_url":"https://api.github.com/repos/michellab/Sire/issues/82/events","html_url":"https://github.com/michellab/Sire/issues/82","id":119711238,"number":82,"title":"analyse_freenrg_mbar is broken","user":{"login":"jmichel80","id":11722212,"avatar_url":"https://avatars.githubusercontent.com/u/11722212?v=3","gravatar_id":"","url":"https://api.github.com/users/jmichel80","html_url":"https://github.com/jmichel80","followers_url":"https://api.github.com/users/jmichel80/followers","following_url":"https://api.github.com/users/jmichel80/following{/other_user}","gists_url":"https://api.github.com/users/jmichel80/gists{/gist_id}","starred_url":"https://api.github.com/users/jmichel80/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmichel80/subscriptions","organizations_url":"https://api.github.com/users/jmichel80/orgs","repos_url":"https://api.github.com/users/jmichel80/repos","events_url":"https://api.github.com/users/jmichel80/events{/privacy}","received_events_url":"https://api.github.com/users/jmichel80/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-12-01T12:54:03Z","updated_at":"2015-12-01T12:54:03Z","closed_at":null,"body":"Using the latest devel version of sire to produce a trajectory, then performing analysis as written below\r\n\r\n[ julien@mechagodzilla: ~/projects/SAMPL/reference/na_cyc/small/12A/discharge/output ]$ cat MBAR.sh \r\n~/sire.app/bin/analyse_freenrg_mbar -i lambda-0.000/simfile.dat lambda-0.125/simfile.dat lambda-0.250/simfile.dat lambda-0.375/simfile.dat lambda-0.500/simfile.dat lambda-0.625/simfile.dat lambda-0.750/simfile.dat lambda-0.875/simfile.dat lambda-1.00/simfile.dat --lam 0.00 0.125 0.250 0.375 0.500 0.625 0.750 0.875 1.00 --temperature 298.0 -o mbar.pmf\r\n[ julien@mechagodzilla: ~/projects/SAMPL/reference/na_cyc/small/12A/discharge/output ]$ bash MBAR.sh \r\n\"/home/julien/sire.app/share/Sire/scripts/analyse_freenrg_mbar.py\" \r\nStarting /home/julien/sire.app/bin/analyse_freenrg_mbar: number of threads equals 16\r\n\r\n# Writing all output to file mbar.pmf\r\nWe are doing a timeseries analysis using the timeseries analysis module in pymbar and will subsample according to that.\r\nWe are doing a timeseries analysis using the timeseries analysis module in pymbar and will subsample according to that.\r\n/home/julien/sire.app/lib/python3.4/site-packages/pymbar/utils.py:70: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.\r\n  if N_k == None:\r\nK (total states) = 9, total samples = 1467\r\nN_k = \r\n[ 163.  163.  163.  163.  163.  163.  163.  163.  163.]\r\nThere are 9 states with samples.\r\nInitializing free energies to zero.\r\nInitial dimensionless free energies with method zeros\r\nf_k = \r\n[ 0.  0.  0.  0.  0.  0.  0.  0.  0.]\r\n/home/julien/sire.app/lib/python3.4/site-packages/scipy/optimize/minpack.py:236: RuntimeWarning: xtol=0.000000 is too small, no further improvement in the approximate\r\n  solution is possible.\r\n  warnings.warn(msg, RuntimeWarning)\r\nFinal dimensionless free energies\r\nf_k = \r\n[ 0.         -0.66327738 -1.3632676  -2.09888765 -2.86906772 -3.67300011\r\n -4.50996649 -5.37941022 -6.28084813]\r\nMBAR initialization complete.\r\nFree energy difference estimated with MBAR is: -3.719440 kcal/mol +/- 0.022837 kcal/mol\r\nFree energy difference estimated with MBAR is: -9.215693 kJ/mol +/- 0.095549 kJ/mol\r\nFree energy difference estimated with TI is: -6.246511 kcal/mol\r\n\r\nThe conversion from kcal/mol to kJ/mol is wrong. \r\nThe TI result is the BAR result times kT. \r\n\r\n"}}