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
>
> _______________________________________________
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> 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>
--
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Received on Fri Dec 28 2012 - 07:00:02 PST
