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
--
========================================
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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