Dear Prof. Case,
Thank you for your response. Your suggested approach
is what I was planning to do, too, except that I was
afraid that the accumulated statistical errors could
be even larger than a single TI calculation.
Best wishes,
Angela
--- "David A. Case" <case.scripps.edu> wrote:
> On Mon, Sep 12, 2005, Angela Liu wrote:
> >
> >
> > I have read and understood your tutorial of
> mutating
> > toluene to nothing. However, in the Amber 8
> manual, it
> > specifies that dummy atoms can only exist in the
> > perturbed Hamiltonian on Page 134 of Section 5.13:
>
> This restriction will be lifted in the next release.
> For now, I think you
> would have to make the change in two steps, one to
> remove certain atoms from
> one end state, and the other to remove atoms from
> the other end state (so that
> the intermediate state is the same for both cases.)
> Then you can arrange it
> so that dummy atoms are only present in the
> perturbed state.
>
> ...good luck...dave case
>
> --
>
>
==================================================================
> David A. Case | e-mail:
> case.scripps.edu
> Dept. of Molecular Biology, TPC15 | fax:
> +1-858-784-8896
> The Scripps Research Institute | phone:
> +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
>
> La Jolla CA 92037 USA |
> http://www.scripps.edu/case
>
==================================================================
>
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Received on Fri Sep 16 2005 - 16:53:03 PDT
