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
> gasphase 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 pathintegral dynamics. Here, since one is taking quantum
> (nuclear) dynamics into consideration, there will be a nontrivial 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 146270216  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
