AMBER Archive (2005)

Subject: Re: AMBER: reverse TI charge perturbation

From: David A. Case (case_at_scripps.edu)
Date: Sat Feb 12 2005 - 18:14:58 CST

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu