[gmx-users] g_wham output

[Schor, M.]

Dear all,

I have used the PULL code in gmx 4 to unwind part of my protein. 10 runs were performed (all pulling the pulled group from 1.3 nm to 4.3 nm away from the reference). The output seems ok from the pullx.xvg and the trajectories. However, when using g_wham to obtain the PMF there seems to be a problem.

The options for pulling in the mdp file:
; PULLING STUFF
pull            = umbrella
pull_geometry   = distance
pull_dim        = n y n
pull_start      = yes
pull_init1      = 0.0
pull_vec1       = 0.0 1.0 0.0
pull_rate1      = 0.005 
pull_ngroups    = 1
pull_group0     = Glu33
pull_group1     = Glu81
pull_k1         = 5000
pull_nstxout    = 500
pull_nstfout    = 500

Using the command (with all the files where they should be)
 g_wham -ix -it -o -hist 
results in the following:
@    title "Umbrella potential"
@    xaxis  label "z"
@    yaxis  label "E (kJ mol\S-1\N)"
@TYPE xy
1.324382e+00    0.000000e+00
1.338367e+00    0.000000e+00
1.352352e+00    0.000000e+00
1.366337e+00    0.000000e+00
....
2.401216e+00    -1.638628e+03
2.415201e+00    -1.730001e+03
2.429185e+00    0.000000e+00
2.443170e+00    -inf
2.457155e+00    -inf
2.471140e+00    -inf
2.485125e+00    -inf
2.499110e+00    -inf
2.513095e+00    -inf
....etc

Using the command (with all the files where they should be)
 g_wham -if -it -o -hist 
results in a more reasonable plot. However, I don't understand what is on the x-axis. I would expect the reaction coordinate (so distance between pulled and reference groups) there, but this doesn't seem to be the case. 

I a post of a very similar problem in the mailing list archive of April 2009. It seems, however, that nobody has answered it. I wondered if anyone has a solution to it now?

Thanks,
Marieke
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