Thank you Brian and Jason! The calculation is still ongoing. I will let you
know the result. -Henry
On Tue, Sep 18, 2012 at 8:11 AM, Brian Radak <radak004.umn.edu> wrote:
> Yet another alternative is to forgo TI entirely and use a re-weighting
> method such as MBAR. The formalism rigorously allows you to extrapolate to
> any arbitrary lambda value regardless of whether you actually generated
> samples in that ensemble or not. Of course, as Jason pointed out, the
> shorter the "distance" in lambda space that you extrapolate the more
> accurate it will be, to the point that eventually the correction is well
> below statistical noise.
>
> The biggest drawback to this approach is the added cost of calculating the
> energy of the samples at all of the other lambda values (which is not part
> of TI). Fortunately, Thomas implemented this type of calculation on the
> fly, see the "ifmbar" and related flags if you are interested (section
> 4.1.3 of the AMBER12 manual).
>
> Regards,
> Brian
>
> On Mon, Sep 17, 2012 at 11:28 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Mon, Sep 17, 2012 at 7:25 PM, <psu4.uic.edu> wrote:
> >
> > > Dear Professor Case,
> > >
> > > This is Henry from Dr. Michael Johnson's lab. In Amber 11/12 user
> > > manual, there is one sentence saying "When using softcore potentials,
> λ
> > > values should be picked so that 0.01 < clambda < 0.99". I am quite
> > > confused why there is such a setting. Could you kindly offer an
> > explanation
> > > or recommended papers for this?
> > >
> >
> > This is not a suggestion for TI in general, but rather a suggestion
> > specifically for the Amber implementation of TI in sander. In order to
> > simplify coding, the mechanism that is used is that 2 separate topology
> > files are used and a separate force calculation is carried out with both
> > topology files (one for each end state). The forces are then scaled by
> > 1/lambda and 1/(1-lambda) for the two end states so they can simply be
> > summed up to give the net force on each atom.
> >
> > This has the advantage that it is very easy to code, but has the
> > disadvantage that the scaling factors go to infinity at the two
> end-points
> > (0 and 1). Therefore, for numerical stability of the Amber
> implementation
> > of TI, you need to select lambda values between 0.99 and 0.01. However,
> > both of these values are very close to their respective end-points, and I
> > would expect that the effect of neglecting the last 0.01 of the
> alchemical
> > coordinate in each direction is well below the noise of the method
> itself.
> >
> >
> > >
> > > One interesting thing is I found my previous error (
> > > http://archive.ambermd.org/201208/0390.html), in which the mask atoms
> > > becomes "a spider monster from space" , is due to clambda < and
> clambda
> > > > 0.99. Alternatively, the softcore potential production run is quite
> > > normal if 0.01 < clambda < 0.99, but not clambda < 0.01 and clambda >
> > 0.99.
> > >
> > > If 0.01 < clambda < 0.99 in softcore potential is true, then is there
> > any
> > > recommended way to set the largest and smallest clamda values for a 12
> > > windows TI run and following Gaussian integration? (The corresponding
> > table
> > > is in Amber 12 user manual's "Table 4.1.: Abscissas and weights for
> > > Gaussian integration<
> > > http://i1076.photobucket.com/albums/w454/happypsu4/table41.png>.")
> > >
> >
> > Sure, just use 0.99 and 0.01 and call them 1 and 0 :). You also don't
> have
> > to use Gaussian integration. There are a number of packages that will do
> > numerical integration for you (I typically use xmgrace) if you don't want
> > to implement your own integration scheme (e.g., trapezoid rule).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > 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
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Received on Mon Sep 24 2012 - 11:30:03 PDT
