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Hi all!
<br />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:
<br />
<p>
<span style="font-family: "Courier New";">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 /></span>
</p>
<p>
<span style="font-family: "Courier New";">pull_k1 = 1000</span>
</p>Output of g_wham:
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<p>
<span style="font-family: "Courier New";"># 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 /></span>
</p>... and so on till end of file
<br />
<br />Any help/ides/solutions are so appreciated!
<br />Regards,
<br />Alex
<br />
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