AMBER Archive (2005)

Subject: Re: AMBER: reverse TI charge perturbation

From: Eric Hu (yhu_2003_at_yahoo.com)
Date: Mon Feb 14 2005 - 18:42:14 CST

Thank you for your clearification.

Eric
--- "David A. Case" <case_at_scripps.edu> wrote:

> On Fri, Feb 11, 2005, Eric Hu wrote:
>
> > As I understand for "reverse perturbation" I
> assinged
> > the inintial charges to be zero on all ligand
> atoms
> > and perturbed into normal charges at lambda = 1.
>
> Note that TI has no "direction" (forward or
> reverse). If you want to reverse
> the roles of lambda=0 and lambda=1 just to test out
> the code (or your
> knowledge of the procedure), that might be
> interesting, but you won't learn
> anything new.
>
> Note that you cannot reverse the roles of lambda=0
> and 1 if there are dummy
> atoms involved: these must always be at lambda=1, as
> explained in the
> Users' Manual.
>
> > of all the energy remains positive in vacume after
> 500
> > NCYC and 1000 MAXCYC comparing to the normal case
> > (charged --> uncharged) whose energy drops
> quickly.
> > Therefore it is easy to understand why the
> following
> > md blows out.
>
> Whether the total energy is positive or negative is
> not in itself of
> significance. It would not by itself make "md blow
> out".
>
> > Then I assign the initial dummy atom types at
> > lambda = 0 and perturb into normal ones at the
> end.
>
> This will fail, for reasons outlined above.
>
> ...dac
>
>
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