Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5.
My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). My peptide is not symmetric, so profile curves are not symmetric, so loosing the sign for COM difference screws my profile curve completely. I did not manage to find any pre-existing answers to this problem from internet. First datalines from pullx files: (sorry for strange file names...) pull_umbr_0.xvg: 0.0000 6.26031 2.27369 pullz_umbr_23.xvg: 0.0000 6.09702 0.0233141 pullz_umbr_50.xvg: 0.0000 6.02097 -2.50088 g_wham command: g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o profile_test.xvg -hist histo_test.xvg -unit kCal My pull code: pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = POPC_POPS ; reference group is bilayer pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 I would appreciate help very much. -Anni -- ************************************************ Anni Kauko, Ph.D. Post Doctoral Researcher Structural Bioinformatics Laboratory Dept. of Biosciences, Biochemistry Åbo Akademi University 20520 Turku, Finland phone: +358 (0)2 215 4006 mobile: +358 (0)50-576 8656 ************************************************
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
