AMBER Archive (2007)

Subject: Re: AMBER: thermodynamic integration

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Nov 08 2007 - 16:42:04 CST

It is not clear in your email on what your system is or what you want to
do. If you use icfe=1, analytically for lambda=1, dv/dl=0, which is not
printed in the .out files. If you use icfe=2, analytically for lambda=0
and lambda=1, dv/dl=0, which is not printed in the .out files.

I have systems where I am doing alchemical changes, and use icfe=2. For
clambda=0 and 1, dv/dl are always zero and are not printed out in the .out
files. For any other lambda value, dv/dl is printed out in the .out files.

On Thu, 8 Nov 2007, Cooper, Matthew wrote:

> Hi,
>
> I am experiencing difficulties with thermodynamic integration in Amber
> 9.
>
> I use the same input deck for numerous integrations. Occasionally, there
> will be no data for DV/DL, though a summary will be printed that
> contains only zeros.
>
> Rerunning the script will sometimes result in DV/DL averages being
> calculated though not always. If I run two molecules with identical
> starting positions but different charges, one may fail while the other
> will not.
>
> Does anyone have any experience with this?
>
> David wrote a while ago, in response to a similar question:
>
> <<Are you sure that the two Hamiltonians are really different? Try a
> one-step
> run with clambda=0, and with clambda=1 to make sure you are really
> getting
> different energies. (The behavior you report, not geting DV/DL at each
> step, but still getting a summary, with all values zero, is consistent
> with not having any energy difference between the two Hamiltonians.)>>
>
> I have checked - the energies are different at clambda = 0 and clambda =
> 1, at least according to the average after 1250 steps.
>
> Thanks,
>
> Matt
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = 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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