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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Received on Mon Feb 25 2013 - 12:30:02 PST
