[gmx-users] Flat energy profile in g_wham
yakovenko_a at ukr.net
Sat Aug 28 01:31:19 CEST 2010
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)"
... and so on till end of file
Any help/ides/solutions are so appreciated!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users