to add to what Zachary said, I'm a little surprised that you need 50
kcal/mol/A restraint if your underlying free energy landscape is so flat
(max values of 0.2 kcal in the results you provided). I'm less concerned
about convergence than I am about your free energy values being so small.
It suggests something isn't set up right. Unfortunately I can't give any
insight into what that might be (other than your WHAM input).
On Tue, Apr 16, 2019 at 3:23 PM Zachary Fallon <
zachary.fallon.stonybrook.edu> wrote:
> Hi Daniel,
>
> I only have a little experience with WHAM analysis, so I would wager some
> of the more veteran users can weigh in here if I miss anything.
>
> Am I understanding you correctly that you varied your r1 and r4 values
> across the different windows? If you go back through the list serve there
> is a good amount of discussion on what to set the r1 and r4 values, and I
> *believe* they should be constant across all of your windows ( I faced
> similar issues as you when I varied my r1 and r4 across windows ). If this
> is wrong I would love for someone to correct me.
>
> Additionally it is typically suggested that your r1 and r4 values be 'far
> away' from your r2/r3 values, to ensure your potential is harmonic at the
> sampled values of your defined coordinate. It is common to set r1 = 1.0 or
> 0.0, and r4 to be some very large number (99.0 or 999). Check out the Amber
> list serve archive for more details on how others have done this, like this
> thread: http://archive.ambermd.org/200705/0113.html.
>
> It is possible that having the r1 and r4 values vary across your windows,
> as well as them being so close to your sampled region, is what is causing
> you trouble. Without knowing much else about your system or setup, that is
> where I would look first. Unfortunately that likely means rerunning your
> simulations.
>
> Finally, it is striking that your system requires a *minimum *of 50
> kcal/(mol*A^2) to maintain your fixed distances. That is a big energy
> penalty, and obviously it may make sense in the context of your system, but
> it sticks out to me as unusual -- whatever barrier you are sampling must be
> huge.
>
> Hope this helps, best of luck!
>
> --Zachary Fallon
>
> On Sat, Apr 13, 2019 at 9:20 AM Daniel Fernández Remacha <
> dnlfr1994.gmail.com> wrote:
>
> > Hi!!
> >
> > I am a student doing a Master Program in Pharmaceutical Chemistry and I
> am
> > writing to get some advice on understanding the results given by WHAM
> after
> > doing an Umbrella Sampling of a dissociation process in a protein (600
> > residues approx.)-peptide interaction.
> >
> > To separate these molecules, a force constant of 50kcal/mol/ang2 (the
> > smallest that can keep the distance reasonably steady) is set, and r1 and
> > r4 values fixed at -1 and +1 unit of each r2=r3 value for every (5 ns
> > production) window. The increment of distance separation from window to
> > window is 0.2 angstroms.
> >
> > The combination of the MD gives a comprehensive separation movement when
> > visualized in VMD and umbrella sampling looks nice since the overlap of
> the
> > simulated windows looks adequate. It is much more full of dots than the
> > example of the tutorial.
> >
> > However, I am having difficulties to understand WHAM results.
> > When looking at the result.dat (as it is called in the AMBER advanced
> > tutorial 17) we get the following data.
> >
> > #Coor Free +/- Prob +/-
> > 7.492857 0.000000 0.000089 0.078953 0.000015
> > 7.678571 0.021163 0.000114 0.076200 0.000018
> > 7.864286 0.048638 0.000050 0.072768 0.000005
> > 8.050000 0.035474 0.000201 0.074392 0.000012
> > 8.235714 0.025529 0.000203 0.075644 0.000032
> > 8.421429 0.074532 0.000235 0.069675 0.000034
> > 8.607143 0.010492 0.000132 0.077576 0.000021
> > 8.792857 0.031564 0.000090 0.074882 0.000009
> > 8.978571 0.138947 0.000127 0.062539 0.000005
> > 9.164286 0.160852 0.000055 0.060283 0.000007
> > 9.350000 0.122887 0.000140 0.064246 0.000019
> > 9.535714 0.063552 0.000138 0.070970 0.000021
> > 9.721429 0.063538 0.000176 0.070971 0.000025
> > 9.907143 0.064124 0.000422 0.070902 0.000016
> > #Window Free +/-
> > #0 0.000000 0.000000
> > #1 0.000000 0.000000
> > #2 0.000000 0.000000
> > #3 0.015216 0.000000
> > #4 0.000000 0.000000
> > #5 0.000000 0.000000
> > #6 0.000000 0.000000
> > #7 0.000000 0.000000
> > #8 0.010285 0.000000
> > #9 0.000000 0.000000
> > #10 0.000000 0.000000
> > #11 0.000000 0.000000
> > #12 0.000000 0.000000
> > #13 0.034936 0.000000
> >
> > The main problem comes when looking at the Free energy, which is used to
> > see whether the system has converged or not. In the WHAM manual, it is
> > mentioned that when this F value is smaller than the specified tolerance
> > the system has converged. The tolerance value set for these results is
> > 10^-6.
> >
> > Moreover, when doing MonteCarlo Bootstrap analysis to look for
> similarities
> > with the information given in the manual, we get 3 iterations; very
> > different from the information given in the WHAM manual.
> >
> > I expected the system to be convergent due to a small increment value,
> > enough simulation time and good overlapping between windows. However, I
> > find strange to see these F values. The files present in the amber
> tutorial
> > do not show these results ( #Window Free and +/-) and the WHAM manual
> does
> > not give information about the example used so we do not have a solid
> > criterion to understand these results.
> >
> > I would be really grateful if you could help me understand the meaning of
> > these results for this system and provide any suggestion to perform a
> > successful umbrella sampling.
> >
> > Thanks in advance,
> >
> > Daniel Fernández
> >
> > PD: We modified the Perl script for minimization, equilibration and
> > production steps and our own script reads coordinates from the end of the
> > last production .rst file window performed; and not from the original
> > coordinates as shown in the tutorial. I am not sure if this is correct
> but
> > we thought that this way the system would be less distorted when reaching
> > high distance values for separation.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Zachary Fallon, PhD Candidate
> Dr. Carlos Simmerling Laboratory
> The Laufer Center for Physical and Quantitative Biology
> The Department of Chemistry, Stony Brook University
> Stony Brook, New York 11794
> Phone: (914) 703-1010 <(914)+703+1010> Email: zachary.fallon.stonybrook.
> <zachary.fallon.stonybrook.edu>edu
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 16 2019 - 13:00:02 PDT
