AMBER Archive (2005)

Subject: Re: AMBER: Re: TI tutorial

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 28 2005 - 10:49:53 CDT

On Tue, Jun 28, 2005, Jiten wrote:
>
> Now looking at the first simple example (charging free energy calculation),
> the PERT.type is same with the TYPE, therfore the perturb charge will not
> be affected. Is it a mistake or the PERT.type shoulb be kept similar with
> what is given in the 2nd example.
>
> [In amber8 manual : An atom isconsidered to be perturbed if its PertType is
> different than its Type.]

Did you read the full paragraph you are quoting (p. 34, top)? Immediately
after the sentence that you quote it says:

"The upshot of this is that you can change the charge of an atom without
making the atom become "perturbed". This fits how sander works: energies with
the perturbed charges are always used (if needed) independent of which atoms
(if any) are marked as "perturbed".

I suppose it could be clearer, but it seems to cover exactly the question you
have.

...good luck...dac

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