[gmx-users] Flat energy profile in g_wham

alexander yakovenko yakovenko_a at ukr.net
Sat Aug 28 01:31:19 CEST 2010

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!  
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