Hi!
Thank you very much for your answers!!
It is our first time in the group using umbrella sampling and WHAM, so any
idea is absolutely appreciated.
To give you a little more context of the system, our idea is to separate a
quite flexible peptide from the protein, from an initial distance of about
7 angstroms to 20 or so, to achieve a full separation of both molecules.
For each increment of 0.2, r1 & r4 move 1unit above and below. We used this
because we thought this way the umbrella potential would be always
symmetrical and equal for each window, allowing sampling with the same
restrictions, and thus, pulling would not alter too much the structure of
the protein. It is more restrictive though.
However, this needed what I mentioned at the end of my previous mail, which
makes sense to me but I am not sure if it is correct. Is it right to start
f.i. the second window (min-equil-prod) from the last prod.rst of the
previous one? I suppose this may be unnecessary if y set r1= 1 and r4= 90,
since the borders always include de starting coordinates.
I will try to simulate the umbrella with the conditions you mention and
compare the results!
Concerning WHAM, the only thing I suspect from is the restraint force. The
AMBER Advanced Tutorial 17 uses the same force as that used for the
umbrella and then multiplies by 2 and applies the conversion to degrees^2.
Is any conversion needed if distance is used instead of an angle? Am I
right if I say that using rk2=rk3=50 kcal/mol/ang, WHAM needs a force
double of what I used in AMBER? This is: 100kcal/mol/ang? No conversion
needed?
Thank you very much again
Daniel Fernández
El mar., 16 abr. 2019 21:23, Zachary Fallon <zachary.fallon.stonybrook.edu>
escribió:
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 17 2019 - 04:30:02 PDT
