AMBER Archive (2007)

Subject: Re: AMBER: TI Approach - mass perturbation

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Dec 11 2007 - 01:47:52 CST

Dear Dave,

Thanks for the information.

Best regards,

On Mon, 10 Dec 2007, David A. Case wrote:

> On Mon, Dec 10, 2007, Ilyas Yildirim wrote:
> >
> > My question is regarding the Thermodynamic Integration implementation
> > in AMBER 9. In the amber mailing list, Petr Kulháne kwrote that in a TI
> > calculation, mass changes are not reflected in perturbation calculations.
> >
> > http://amber.ch.ic.ac.uk/archive/200504/0432.html
>
> Note that this comment has to do with earlier versions of Amber, which carried
> out TI calculations in a different fashion.
>
> For Amber 9, please see the last paragraph on p. 153 of the Users' Manual.
> In classical mechanics, the Boltzmann distribution of configurations (and
> hence all averages like <DV/DL>) are independent of the masses. We
> arbitrarily decide to use the masses in the prmtop file for the first group.
> (This is enforced in mdread.f.)
>
> This does mean that the actual trajectories that you get on going from 0->1
> will differ from those on going from 1->0, but any converged statistical
> averages will be the same. Note that, following classical dynamics, we don't
> even bother to calculate kinetic energy terms, since they should cancel in any
> legitimate thermodynamic cycle.
>
> > Does that mean that I cannot
> > do any mass perturbation (like a perturbation from oxygen to nitrogen) in
> > TI Approach?
>
> No: you certainly can to transformations that include changes in masses. As
> always, you have to subtract two sides of a thermodynamic cycle (such as a
> transformation in solution vs. one in an enzyme, or a transfomation in
> gas-phase vs. one in solution) in order to get a physically meaningful number.
>
> [Amber 10 will have the ability to carry out thermodynamic integration on the
> masses for path-integral dynamics. Here, since one is taking quantum
> (nuclear) dynamics into consideration, there will be a non-trivial kinetic
> energy contribution to the partition function, and this can be used to
> estimate kinetic isotope effects and equilibrium isotope partitioning. Or,
> it could be used as part of an "alchemy" change (such as N to O, etc.)]
>
> ...hope this helps....dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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