[gmx-users] Flat energy profile in g_wham

[Justin A. Lemkul]

alexander yakovenko wrote:
>   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
> 

What does your histogram look like?  Do you have sufficient overlap between 
neighboring windows?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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