Re: amber-developers: Broken TI Test cases (icfe=2)

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Fri, 21 Dec 2007 19:01:04 -0500 (EST)

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
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------
Received on Sun Dec 23 2007 - 06:07:36 PST
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