[gmx-users] Flat energy profile in g_wham

[Justin A. Lemkul]

alexander yakovenko wrote:
>   Hi Justin!
> Thank you for replay. My histogram (can send if required) consists of 13 
> windows (0.1 and 0.2nm sampling) and look like two peaks (with 
> amplitudes 3-4e+2) separated with a valley of 1.2-1.5e+2 (my protein has 
> two sub-domains so should be OK) and smallest overlap between windows is 

I don't understand this description.  How can 13 windows produce only two peaks?

To post an image, please see bullet point #4 here:

http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette

> 1e+2 by amplitude. So I am expecting something like M-shaped PMF profile 
> instead of flat line. Can the problem be in directions of pulling code 
> as I am using a distance as reaction coordinate, not an axis?

In principle, you should be able to pull any which way you like, so I don't see 
that as a problem.

-Justin

> Regards,
> Alex
> 
> 
>     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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