[gmx-users] Re: Re[7]: Flat energy profile in g_wham

[alexander yakovenko]

 Sorry for mixing things, I do pull into N Y N direction and then
   performed umbrella simulation at Y Y Y for each distances window. 
   This is very good question, actually I don't realize it too. The only
   thing what I can say is that I haven't edited/renamed these files,
   just copy them. So this is pure output of mdrun, hopes it knows what
   it writes... I can provide a tpr of a window for example so you can
   check couple first strings (for reproduction, I carried out all
   calculations on 8x Xeons at 2.66 workstations).
   Alex
   >

   First, you confuse me when you say "pulling direction was along  
   Y-axis" since your .mdp file indicates pull_dim = Y Y Y and so you are  
   pulling in *all* dimensions.
   
   Your profile doesn't look like mine at all, but then again I took mine  
   from a force profile. Now that I can see your forces and  
   displacements, I can't find any match between them. For example:
   cneale at cneale-desktop:~/work/August2010/integral/u10$ tail pullf_u10.xvg
   11982.0000      255.769
   11984.0000      332.586
   11986.0000      291.367
   11988.0000      264.031
   11990.0000      330.69
   11992.0000      336.757
   11994.0000      327.46
   11996.0000      475.078
   11998.0000      440.766
   12000.0000      342.814
   cneale at cneale-desktop:~/work/August2010/integral/u10$ tail pullx_u10.xvg
   11982.0000      3.05189 4.39188 -1.23643        2.03259 2.62201 3.35563
   11984.0000      3.12086 4.37951 -1.63297        1.98567 2.64212 -3.25943
   11986.0000      3.13274 4.37699 -1.57303        1.97354 2.64089 -3.32607
   11988.0000      3.13754 4.38542 -1.52275        1.94917 2.63444 -3.38366
   11990.0000      3.12712 4.38416 -1.61647        1.93608 2.63691 -3.29597
   11992.0000      3.11342 4.37694 -1.59735        1.95931 2.61705 -3.28952
   11994.0000      3.0957  4.384   -1.5691 1.99226 2.57634 -3.3149
   11996.0000      3.08384 4.38684 5.24141 2.00727 2.57168 -3.09875
   11998.0000      2.99618 4.41111 5.25558 2.08776 2.53869 -3.1227
   12000.0000      2.79826 4.41958 5.22444 2.29862 2.53084 -3.12472
   
   
   Can you explain to me how these can match up (with an equation please)?
   
   
   Quoting alexander yakovenko <   yakovenko_a at ukr.net   >:
   
   > Yep, it was mistake with a sign, is   
   >    http://picasaweb.google.ca/117558205101329348732/G_wham#5511351478636719042      
   > looks like your one? Btw my temperature was 310K.
   > The dollars you would lost (as I used only 1 mdp for all runs via   
   > script and thus avoiding humans mistakes like with pictures) is   
   > probably because complicated landscape - the dissociation is coupled  
   >  to (partial) unfolding and relative sub-domains shift (actually  
   > this  experiment is aimed to support this hypothesis). I.e. it does  
   > not  look too suspicious for me; something closer to manual was  
   > expected  though. Anyway I attach logs from all my simulations and  
   > the mdp.
   > As for box, it has 10x16x7 edges and pulling direction was along   
   > Y-axis to bring molecules only 5.5nm apart (DNA and protein of ~2 nm  
   >  radii) so there is definitely sufficient distances.
   > Anyway the only bug in g_wham is an explanation I can give to   
   > ABSOLUTELY flat line of PMF profile.
   > As for colors, can we please stick on windows ids instead? I guess   
   > you told about w4, w6 and w8 so I attached their logs from mdrun and  
   >  for w10 too.
   > P.S. I still not understand if there is a way to make g_wham working  
   >  for me (suggesting all other calculations were made fairly)?
   > Alex
   >
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