[gmx-users] Re: gmx-users Digest, Vol 76, Issue 164
yakovenko_a at ukr.net
Mon Aug 30 00:35:45 CEST 2010
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 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?
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!
What does your histogram look like? Do you have sufficient overlap between
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