Re: [AMBER] Question in umbrella sampling

From: Aron Broom <broomsday.gmail.com>
Date: Mon, 31 Dec 2012 17:54:46 -0500

Oh wait, I am just confused, the division makes no sense.
On Dec 31, 2012 5:53 PM, "Aron Broom" <broomsday.gmail.com> wrote:

> Yeah, I was hoping the factor of two would explain the probability issue,
> that is really weird. What is the sum of the probabilities?
>
> The thing is that in WHAM it expects F = 0.5kx**2 but isn't AMBER F =
> kx**2 and therefore you should actually DIVIDE all your values by 2 rather
> than multiply?
>
> Maybe I,m just confused
> On Dec 29, 2012 8:54 PM, "Sajeewa Pemasinghe" <sajeewasp.gmail.com> wrote:
>
>> Thanks Aron,
>>
>> Yes I have considered the factor of two (when giving the input file to the
>> wham program I multiplied the the force constant which I gave to AMBER by
>> two).
>>
>> Yes there is a ligand binding to this protein. But as Daniel has pointed
>> out the total probability has exceeded one
>>
>> 10.950000 0.000000 -nan 0.860969 -nan
>> 34.350000 0.000000 -nan 0.860969 -nan
>>
>> I have followed the tutorial and the manual in wham as closely as possible
>> and can't figure out why this happened.
>>
>> Thank you
>>
>> Sajeewa Dewage
>>
>> On Sat, Dec 29, 2012 at 5:36 PM, Aron Broom <broomsday.gmail.com> wrote:
>>
>> > 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
>> > > >
>> > > _______________________________________________
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>> > >
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Received on Mon Dec 31 2012 - 15:00:03 PST
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