I believe the option is called "ialtd". But in reading the AMBER12 manual,
it seems that is now the default anyway, so no worries.
That's excellent that there is a nicer way to specify the harmonic now.
~Aron
On Mon, Feb 25, 2013 at 4:07 PM, Brian Radak <radak004.umn.edu> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ 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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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Feb 25 2013 - 15:00:04 PST
