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
First, I don't think that you converted and debiased correctly. Once
you have a histogram of the displacement, then you will debias that
histogram like this (assuming run at 298K):
FC=1000
T=298
cat biased.hist |awk '{print
$1,-0.00831447*'${T}'*log($2)-0.5*'${FC}'*$1*$1}' > debiased.hist
You attached the force file, not the coordinate file. I tried to
convert like this:
cat pullf_u10.xvg|grep -v '[@|#]' |awk '{print $1,-($2/1000)}'
and then I made a histogram and then I converted to energy and
debiased, but I got something entirely different than yours.
I would bet dollars to donoughts that either your force constant was
not 1000 or your sampling is otherwise messed up. Can you post the
coord.xvg from that same window?
What are your .mdp options? if your cutoffs are shorter than 3 nm then
your 2 molecules are not going to see each other (unless you have
PME). This is one reason you might get a relatively flat PMF.
Nevertheless, a perfectly flat PMF is certainly an error! (where's the
noise?)
My main concern is that your sampling is incorrect for some reason. To
see this, look at your original set of probability histograms at
http://picasaweb.google.ca/117558205101329348732/G_wham#5511244561053627250
See the cyan peak on the left half? now look below it and you'll see a
green (and a purple) histogram line that is half the height and twice
the width, but is in nearly the same spot. This is suggestive of
massive unconvergence, so massive that you have probably done
something wrong.
Please go back through your runs and see if you might have set
something up incorrectly. If you still think that it's correct, then
please *cut and paste* sections of your setup for that cyan peak and
for the green histogram below it (e.g. pull code options in .mdp file,
commands for mdrun, etc.) and send all of that to the mailing list.
Quoting alexander yakovenko <yakovenk...@ukr.net>:
0. Thank you all who spent time answering my post (and especially
for explanations how to convert bins into energy)!
1. Yes, force is 1000 kJ/mol/nm^2 in all windows
2. z is in nm as default in wham
3. I made profile for w#10 (just in the case I attach forces file).
the picture of window profile is there
http://picasaweb.google.ca/117558205101329348732/G_wham#5511315785714749378.
Thank you once more!
P.S. Looks like (some of) you are not surprised with zeros in my
wham output, but cant you please explain me what is wrong there?
P.P.S. Resending message again because of server error, sorry for
possible duplication.
Alex
Alexander, please post the following:
1. force constants for your plot at
http://picasaweb.google.ca/117558205101329348732/G_wham#5511287294315721970
NOTE: if they are all 1000 as in your first post, then you have a
problem in your sampling.
2. units for your x-axis in the plot mentioned in part 1, above (i.e.
angstroms or nanometers?)
3. convert one (only one) of your sampling probability histograms to
an energy histogram and debias it (without using wham). To convert to
energy, take each histogram bin and apply E=-kB*T*ln(P). Now debias by
subtracting E_rest=0.5*Fc*(r-r0). You will have noise at each end, but
what about the middle part, is it flat or not? Post a picture of this
please.
Chris
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