1) make sure your force constants are correct, there is an important factor
of 2 difference between AMBER and WHAM.
2) the results are just saying that you have a deep energy minimum there,
if this is
Iigand binding a protein it makes perfect sense.
~Aron
On Dec 28, 2012 10:16 AM, "Sajeewa Pemasinghe" <sajeewasp.gmail.com> wrote:
> Thank you very much. I will go through it .
>
> On Fri, Dec 28, 2012 at 9:37 AM, Daniel Sindhikara <sindhikara.gmail.com
> >wrote:
>
> > Questions regarding Grossfields WHAM program might be better directed
> > towards him.
> > But looking at your output it appears to have a serious numerical
> problem,
> > did you notice
> > that the total probability is greater than 1?
> > Look at these two lines:
> >
> > 10.950000 0.000000 -nan 0.860969 -nan
> > 34.350000 0.000000 -nan 0.860969 -nan
> >
> > It's hard to tell if the problem is in your script or the WHAM code
> though.
> >
> >
> > I have code that will work on this system but haven't made an example yet
> > for all types of
> > umbrella sampling in AMBER. If you are interested please see:
> >
> http://dansindhikara.com/Software/Entries/2012/3/9_Modular_Reweighting.html
> > and contact me directly for questions.
> >
> >
> > 2012/12/28 Sajeewa Pemasinghe <sajeewasp.gmail.com>
> >
> > > Dear all,
> > >
> > > I am trying to calculate PMF(potential of mean force) along a distance
> > > using AMBER. I have done 97 simulations placing a particular molecule
> at
> > 97
> > > different points along the distance coordinate. The distance
> > distributions
> > > show considerable overlap as can be seen by the reaction.histogram
> which
> > I
> > > have attached. I am using Professor Grossfield's 'wham' program to
> > > calculate the PMF.
> > >
> > > The problem is, when PMF is calculated with the command
> > >
> > > ./wham 10.8 34.2 78 0.0001 300.0 1 metadatafile
> 97_20k.pmf
> > >
> > > 97_20k.log
> > >
> > >
> > > almost all the probability (0.860969) gets concentrated at 10.95.
> > >
> > > #Coor Free +/- Prob +/-
> > > 10.650000 7.808876 -nan 0.000002 -nan
> > > 10.950000 0.000000 -nan 0.860969 -nan
> > > 11.250000 1.212829 -nan 0.112086 -nan
> > > 11.550000 2.240838 -nan 0.019909 -nan
> > > 11.850000 3.006684 -nan 0.005495 -nan
> > > 12.150000 3.936132 -nan 0.001152 -nan
> > > 12.450000 4.999682 -nan 0.000193 -nan
> > > 12.750000 5.516777 -nan 0.000081 -nan
> > > 13.050000 5.907733 -nan 0.000042 -nan
> > > 13.350000 7.185598 -nan 0.000005 -nan
> > > 13.650000 7.481728 -nan 0.000003 -nan
> > > 13.950000 7.616759 -nan 0.000002 -nan
> > > 14.250000 7.791042 -nan 0.000002 -nan
> > > 14.550000 7.257627 -nan 0.000004 -nan
> > > 14.850000 7.699594 -nan 0.000002 -nan
> > > 15.150000 8.394635 -nan 0.000001 -nan
> > > 15.450000 8.435193 -nan 0.000001 -nan
> > > 15.750000 8.319693 -nan 0.000001 -nan
> > > 16.050000 7.899175 -nan 0.000001 -nan
> > > 16.350000 7.520675 -nan 0.000003 -nan
> > > 16.650000 7.350089 -nan 0.000004 -nan
> > > 16.950000 7.144262 -nan 0.000005 -nan
> > > 17.250000 6.815532 -nan 0.000009 -nan
> > > 17.550000 6.926580 -nan 0.000008 -nan
> > > 17.850000 7.360287 -nan 0.000004 -nan
> > > 18.150000 7.322875 -nan 0.000004 -nan
> > > 18.450000 7.640881 -nan 0.000002 -nan
> > > 18.750000 8.092909 -nan 0.000001 -nan
> > > 19.050000 8.263583 -nan 0.000001 -nan
> > > 19.350000 8.647279 -nan 0.000000 -nan
> > > 19.650000 9.453315 -nan 0.000000 -nan
> > > 19.950000 9.621312 -nan 0.000000 -nan
> > > 20.250000 9.819468 -nan 0.000000 -nan
> > > 20.550000 9.990643 -nan 0.000000 -nan
> > > 20.850000 10.504337 -nan 0.000000 -nan
> > > 21.150000 10.727750 -nan 0.000000 -nan
> > > 21.450000 10.831247 -nan 0.000000 -nan
> > > 21.750000 10.968361 -nan 0.000000 -nan
> > > 22.050000 11.483583 -nan 0.000000 -nan
> > > 22.350000 11.713253 -nan 0.000000 -nan
> > > 22.650000 12.165046 -nan 0.000000 -nan
> > > 22.950000 12.440480 -nan 0.000000 -nan
> > > 23.250000 12.481515 -nan 0.000000 -nan
> > > 23.550000 12.357771 -nan 0.000000 -nan
> > > 23.850000 12.082079 -nan 0.000000 -nan
> > > 24.150000 11.797020 -nan 0.000000 -nan
> > > 24.450000 11.701011 -nan 0.000000 -nan
> > > 24.750000 11.550476 -nan 0.000000 -nan
> > > 25.050000 11.047749 -nan 0.000000 -nan
> > > 25.350000 10.919919 -nan 0.000000 -nan
> > > 25.650000 11.163292 -nan 0.000000 -nan
> > > 25.950000 11.053891 -nan 0.000000 -nan
> > > 26.250000 10.481810 -nan 0.000000 -nan
> > > 26.550000 10.423612 -nan 0.000000 -nan
> > > 26.850000 10.313436 -nan 0.000000 -nan
> > > 27.150000 10.132487 -nan 0.000000 -nan
> > > 27.450000 9.918259 -nan 0.000000 -nan
> > > 27.750000 9.663974 -nan 0.000000 -nan
> > > 28.050000 9.614350 -nan 0.000000 -nan
> > > 28.350000 9.817018 -nan 0.000000 -nan
> > > 28.650000 9.833279 -nan 0.000000 -nan
> > > 28.950000 9.848224 -nan 0.000000 -nan
> > > 29.250000 10.232477 -nan 0.000000 -nan
> > > 29.550000 10.054117 -nan 0.000000 -nan
> > > 29.850000 9.692431 -nan 0.000000 -nan
> > > 30.150000 9.123378 -nan 0.000000 -nan
> > > 30.450000 8.852411 -nan 0.000000 -nan
> > > 30.750000 8.441608 -nan 0.000001 -nan
> > > 31.050000 8.014642 -nan 0.000001 -nan
> > > 31.350000 7.693466 -nan 0.000002 -nan
> > > 31.650000 7.795882 -nan 0.000002 -nan
> > > 31.950000 8.136751 -nan 0.000001 -nan
> > > 32.250000 8.386743 -nan 0.000001 -nan
> > > 32.550000 8.583118 -nan 0.000000 -nan
> > > 32.850000 8.899569 -nan 0.000000 -nan
> > > 33.150000 8.909652 -nan 0.000000 -nan
> > > 33.450000 8.861119 -nan 0.000000 -nan
> > > 33.750000 8.516236 -nan 0.000001 -nan
> > > 34.050000 7.808876 -nan 0.000002 -nan
> > > 34.350000 0.000000 -nan 0.860969 -nan
> > >
> > > #Window Free +/-
> > > #0 0.000000 -nan
> > > #1 0.558498 -nan
> > > #2 1.130566 -nan
> > > #3 1.756719 -nan
> > > #4 2.698522 -nan
> > > #5 3.090608 -nan
> > > #6 3.397631 -nan
> > > #7 4.138555 -nan
> > > #8 4.492565 -nan
> > > #9 4.955348 -nan
> > > #10 5.170213 -nan
> > > #11 5.258698 -nan
> > > #12 5.255078 -nan
> > > #13 5.055978 -nan
> > > #14 4.957377 -nan
> > > #15 5.323800 -nan
> > > #16 5.710866 -nan
> > > #17 5.962826 -nan
> > > #18 5.976558 -nan
> > > #19 5.768377 -nan
> > > #20 5.506420 -nan
> > > #21 5.261064 -nan
> > > #22 5.010233 -nan
> > > #23 4.811257 -nan
> > > #24 4.638065 -nan
> > > #25 4.471429 -nan
> > > #26 4.504458 -nan
> > > #27 4.682320 -nan
> > > #28 4.877600 -nan
> > > #29 4.931259 -nan
> > > #30 5.149352 -nan
> > > #31 5.395898 -nan
> > > #32 5.741836 -nan
> > > #33 6.007907 -nan
> > > #34 6.290791 -nan
> > > #35 6.925992 -nan
> > > #36 7.159492 -nan
> > > #37 7.354654 -nan
> > > #38 7.481433 -nan
> > > #39 7.771686 -nan
> > > #40 8.057583 -nan
> > > #41 8.306121 -nan
> > > #42 8.392598 -nan
> > > #43 8.539776 -nan
> > > #44 8.751357 -nan
> > > #45 9.152848 -nan
> > > #46 9.347933 -nan
> > > #47 9.738337 -nan
> > > #48 9.938098 -nan
> > > #49 10.036732 -nan
> > > #50 9.932958 -nan
> > > #51 9.683884 -nan
> > > #52 9.505475 -nan
> > > #53 9.370011 -nan
> > > #54 9.287224 -nan
> > > #55 9.184366 -nan
> > > #56 8.969140 -nan
> > > #57 8.703106 -nan
> > > #58 8.574605 -nan
> > > #59 8.561688 -nan
> > > #60 8.663351 -nan
> > > #61 8.658094 -nan
> > > #62 8.439430 -nan
> > > #63 8.153154 -nan
> > > #64 8.007116 -nan
> > > #65 7.943718 -nan
> > > #66 7.849646 -nan
> > > #67 7.727590 -nan
> > > #68 7.592033 -nan
> > > #69 7.514357 -nan
> > > #70 7.361412 -nan
> > > #71 7.292273 -nan
> > > #72 7.229384 -nan
> > > #73 7.242339 -nan
> > > #74 7.341128 -nan
> > > #75 7.401717 -nan
> > > #76 7.415802 -nan
> > > #77 7.499715 -nan
> > > #78 7.676263 -nan
> > > #79 7.624492 -nan
> > > #80 7.253869 -nan
> > > #81 6.916200 -nan
> > > #82 6.544325 -nan
> > > #83 6.312646 -nan
> > > #84 5.902258 -nan
> > > #85 5.633176 -nan
> > > #86 5.347762 -nan
> > > #87 5.336276 -nan
> > > #88 5.432574 -nan
> > > #89 5.626945 -nan
> > > #90 5.820900 -nan
> > > #91 5.980173 -nan
> > > #92 6.126139 -nan
> > > #93 6.295844 -nan
> > > #94 6.444728 -nan
> > > #95 6.473352 -nan
> > > #96 6.409720 -nan
> > >
> > >
> > >
> > >
> > > I have tried hard to understand what is going on but couldn't come up
> > with
> > > an explanation. If anyone could please give me some guidance to
> overcome
> > > this issue I would be highly obliged.
> > >
> > > Thank you very much
> > >
> > > Sajeewa Dewage
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
> > Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
> > sindhikara.gmail.com <http://www.dansindhikara.com>
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Dec 29 2012 - 15:00:02 PST
