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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. <br>
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@2.66 workstations).<br>
Alex<br>
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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@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@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 <<a href="mailto:yakovenko_a@ukr.net">yakovenko_a@ukr.net</a>>:
> Yep, it was mistake with a sign, is
> <a href="http://picasaweb.google.ca/117558205101329348732/G_wham#5511351478636719042">http://picasaweb.google.ca/117558205101329348732/G_wham#5511351478636719042</a>
> 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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