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, ë
> 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
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Received on Mon Sep 17 2012 - 20:30:02 PDT
