[gmx-users] Re: gmx-users Digest, Vol 76, Issue 164

[alexander yakovenko]

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?  
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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