One advantage of doing it this way, at least if you compute the error
associated with each step, is that you'll know where you have the largest
error, and can reduce your overall error by doing more sampling on that
step. Of course, you do have to run more simulations this way...
On 9/16/05, Angela Liu <angela_ambermail.yahoo.com> wrote:
>
> 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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>
>
>
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Received on Fri Sep 23 2005 - 20:53:01 PDT
