Dear Dr. Thomas :
Here is my TI result:
lambda dvdl
0.01 46.26
0.05 15.14
0.10 1.20
0.15 -11.11
0.20 -14.88
0.25 -13.20
0.30 -14.49
0.35 -13.81
0.40 -12.96
0.45 -5.11
0.50 -0.24
0.55 5.50
0.60 8.88
0.65 12.97
0.70 11.61
0.75 14.85
0.80 11.63
0.85 12.46
0.90 0.70
0.95 -22.85
0.99 -54.70
the dvdl curve near lambda 0 or 1 seems to be rather steep, far from
linear. Is it normal?
What reason may cause such result?
Best Regards!
Denis
2012/7/26 <steinbrt.rci.rutgers.edu>
>
> Hi,
>
> > The post http://archive.ambermd.org/201002/0108.html </>said softcore
> > cannot use at lambda <0.01 or >0.99,
> > Does it support now?
>
> no, that limitation has not changed. There is some work in progress to
> make a new version of TI that would allow l=0/1, but it is not finished
> yet. However, I have never seen this as really problematic. The dvdl curve
> should be linear at both ends and you really want the integral over it, so
> using 0.01 or 0.00 as a fixed-point for numerical integration amounts to
> the same thing. Unless you want more than a hundred lambda-windows, there
> is no real gain from simulating in the <0.01 / >0.99 region.
>
> > If I want to get the point at Lambda=0, do I have to use "hardcore"?
>
> if you really want this point, then yes, you can not use soft core
> potentials.
>
> > Can I mix the result using hardcore at 0 or 1 and using softcore at other
> > lambda? In other words, at lambda=0 or 1, does softcore and hardcore give
> > out the same result theoretically?
>
> No! Far from it actually, the two approaches amount to very different
> potential functions and should not even be close in terms of curve shape.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Wed Aug 08 2012 - 10:30:02 PDT
