Dave,
I have analyzed some systems using icfe=2, and I have seen that it is
better than icfe=1 when you have dummy atoms in initial/final states.
The convergency around lambda=0 is improved with icfe=2 compared to icfe=1
option when you have dummy atoms present in the initial state. We will
submit a paper pretty soon which uses icfe=2 option.
There are a couple of other systems I have been working on and will
probably submit another paper describing some experimental results with
AMBER9's icfe=2 option (there are dummy atoms in initial and final states
in those systems).
In my systems, I do not turn on/off any atoms; I am doing alchemical
transformations from one atom (type) to another. People who are turning
on/off the vdW parameters might have problems with icfe option and
softcore potentials might be a must to use for those systems. But for the
others (like the systems I am analyzing), I think that icfe is useful.
I did not do any calculations using the softcore potential option of
AMBER10; so I cannot compare it with the results I am getting with icfe=2.
Best,
As you know, icfe is mixing the
On Fri, 21 Dec 2007, David A. Case wrote:
> On Fri, Dec 21, 2007, Ilyas Yildirim wrote:
> >
> > Is there any reason why icfe=2 is removed from AMBER10?
>
> As far as I can see, the softcore options eliminate the need for icfe=2
> (and probably for klambda>1 as well).
>
> I'm certainly open to counter-arguments. But making both the code and the
> documentation simpler has its appeal.
>
> Let me know what you think....dave
>
>
--
Ilyas Yildirim
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= Department of Chemistry - =
= University of Rochester - =
= Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
= http://www.pas.rochester.edu/~yildirim/ =
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Received on Sun Dec 23 2007 - 06:07:36 PST
