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Hi Justin!
<div>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?
<br /></div>Regards,
<br />Alex
<br />
<br />
<br />
<blockquote class="ukr_editor_quotation" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">alexander yakovenko wrote:
<br />> Hi all!
<br />> there is a question about g_wham from gmx 4.0.5. I am integrating
<br />> trajectory of dissociation of protein-DNA complex. All goes well but PMF
<br />> profile from g_wham looks as straight line. Double check of pullf and
<br />> pullx files showed that mdrun worked properly, forces are OK and
<br />> reasonably distributed. It looks like g_wham can't sample data properly
<br />> or I do something wrong. My pull code:
<br />>
<br />> pull = umbrella
<br />> pull_geometry = distance
<br />> pull_dim = Y Y Y
<br />> pull_start = yes
<br />> pull_ngroups = 1
<br />> pull_group0 = dna
<br />> pull_group1 = rot
<br />> pull_init1 = 0.0
<br />> pull_rate1 = 0.0
<br />>
<br />> pull_k1 = 1000
<br />>
<br />> Output of g_wham:
<br />>
<br />> # This file was created Fri Aug 27 16:07:45 2010
<br />> # by the following command:
<br />> # g_wham_d -it ug5d_it.dat -if ug5d_if.dat
<br />> #
<br />> # g_wham_d is part of G R O M A C S:
<br />> #
<br />> # Grunge ROck MAChoS
<br />> #
<br />> @ title "Umbrella potential"
<br />> @ xaxis label "z"
<br />> @ yaxis label "E (kJ mol\S-1\N)"
<br />> @TYPE xy
<br />> 3.105821e+00 0.000000e+00
<br />> 3.122188e+00 -1.690245e+03
<br />> 3.138555e+00 -1.690245e+03
<br />> 3.154921e+00 -1.690245e+03
<br />>
<br />> ... and so on till end of file
<br />>
<br />> Any help/ides/solutions are so appreciated!
<br />> Regards,
<br />> Alex
<br />>
<br />
<br />What does your histogram look like? Do you have sufficient overlap between
<br />neighboring windows?
<br />
<br />-Justin</blockquote>
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