I believe that is correct about the force constant correction. I think
you've also got the input file correct, but you should make sure that the
shape of potential is correct. Although it likely won't impact you, since
your r1 and r4 are really far from your r2 and r3 (a good thing) the
default shape in AMBER is meant for refining NMR structures, and so while
it has proper harmonic restraint shaped walls up until r1 and r4, after
that it becomes linear. There is an option to ensure it is continually
harmonic shaped, and it's probably good practice to turn that on if you
haven't already started your simulations.
You should also quickly visualize your reaction coordinate trajectories all
at once in something like xmgrace, and ensure that you have complete
coverage of the reaction coordinate (i.e. no regions that are not well
sampled, and substantial overlap in the exploration of each window). This
is general good practice, but particularly in your case since you have what
I would consider a GIGANTIC force constant. Such a high force constant
will mean the deviations from that value in each simulation will be very
small (likely much less than 1 angstrom), and so I would actually expect
many of your windows don't really overlap, which is necessary for accurate
umbrella sampling.
~Aron
On Mon, Feb 25, 2013 at 3:09 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> Hello all. I am trying to calculate the pmf from pulling two protein units
> apart from each other. For this I am using the umbrella sampling method to
> slowly pull the structures apart. I have performed 35 separate simulations,
> each with a different equilibrium distance between the two COM of the two
> protein units, in which I separate the two structures 1 angstrom at a time.
> In other words. For each dist.RST file the r2 and r3 values are the same
> and for every subsequent simulation this value increase by 1 angstrom. I
> have started with 9 angstroms and ended at 33. The force constants, k2 and
> k3, were set to 60 .
> I have set r1 = -30 and r4 = 60 so that the bottom of the potential was
> centred at 15. Is this correct? This means that r2 = r3 = distance that
> changes from 9 to 33.
> Now my doubt lies in how should I calculate the PMF using WHAM. I have
> followed the amber tutorial A17, and as far as I could understand, the wham
> program assumes that the biasing potential is of the form V = 1/2k(x - x0
> )^2 . The biasing potential described in amber manual (page 204) is k2 (R -
> r2 )^2. Is this the correct potential to consider? If yes, does this mean
> that the force constant I should tell the wham program to use is 120 and
> not 60?
> Thank you
> Fabrício
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Feb 25 2013 - 13:30:02 PST
