Hi Justin! Thank you for replay. My histogram (can send if required) consists of 13 windows (0.1 and 0.2nm sampling) and look like two peaks (with amplitudes 3-4e+2) separated with a valley of 1.2-1.5e+2 (my protein has two sub-domains so should be OK) and smallest overlap between windows is 1e+2 by amplitude. So I am expecting something like M-shaped PMF profile instead of flat line. Can the problem be in directions of pulling code as I am using a distance as reaction coordinate, not an axis? Regards, Alex alexander yakovenko wrote: > Hi all! > there is a question about g_wham from gmx 4.0.5. I am integrating > trajectory of dissociation of protein-DNA complex. All goes well but PMF > profile from g_wham looks as straight line. Double check of pullf and > pullx files showed that mdrun worked properly, forces are OK and > reasonably distributed. It looks like g_wham can't sample data properly > or I do something wrong. My pull code: > > pull = umbrella > pull_geometry = distance > pull_dim = Y Y Y > pull_start = yes > pull_ngroups = 1 > pull_group0 = dna > pull_group1 = rot > pull_init1 = 0.0 > pull_rate1 = 0.0 > > pull_k1 = 1000 > > Output of g_wham: > > # This file was created Fri Aug 27 16:07:45 2010 > # by the following command: > # g_wham_d -it ug5d_it.dat -if ug5d_if.dat > # > # g_wham_d is part of G R O M A C S: > # > # Grunge ROck MAChoS > # > @ title "Umbrella potential" > @ xaxis label "z" > @ yaxis label "E (kJ mol\S-1\N)" > @TYPE xy > 3.105821e+00 0.000000e+00 > 3.122188e+00 -1.690245e+03 > 3.138555e+00 -1.690245e+03 > 3.154921e+00 -1.690245e+03 > > ... and so on till end of file > > Any help/ides/solutions are so appreciated! > Regards, > Alex > What does your histogram look like? Do you have sufficient overlap between neighboring windows? -Justin
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