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 xe...@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: cne...@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 cne...@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 < yakovenk...@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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