Yes, that should be correct.
Also, a nifty recent feature in AMBER (sander only) is that you can instead
set r0 and k0 in the DISANG file. This will automatically set r1-r4 and
rk2/rk3 to be appropriate for a harmonic potential when considering the
coordinate type (i.e. distance, torsion, etc.)
Regards,
Brian
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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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Mon Feb 25 2013 - 14:00:03 PST
