I met the same problem when using 4.5.1 for some systems, the PMF shows zero curve, while the hist file looks fine. The problem disappears when using 4.5.2. Jianguo
________________________________ From: Susana Tomasio <[email protected]> To: [email protected] Sent: Wednesday, 9 March 2011 20:07:25 Subject: [gmx-users] Zero Potential of Mean Force with g_wham Dear all, I am running umbrella sampling of a molecule through a lipid bilayer with gromacs 4.5.1. When I extracted the potential of mean force with g_wham I got zero for all the windows. Any ideas of why this is happening? This is the command I used: g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist And this is the pull code of my .mdp file: ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Bilayer pull_group1 = Protein pull_vec1 = 0 0 0 pull_init1 = 0 0 0 pull_rate1 = 0 pull_pbcatom0 = 1453 pull_pbcatom1 = 13187 pull_k1 = 3000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps Thank you. Best regards, Susana
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
