Hello Aron. Thank you for the advice. I just could not find the option to
ensure that the potential is continually harmonic shaped. Is it in the nmr
section?
Thank you
Fabrício
2013/2/25 Aron Broom <broomsday.gmail.com>
> 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 - 14:00:02 PST
