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
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