Re: [AMBER] QMMM NEB reaction pathway calculation with AMBER

From: Teerapong Pirojsirikul <tpirojsi.ucsd.edu>
Date: Mon, 30 Jun 2014 11:17:51 -0700

Thank you for your comments Jason. That makes more sense to me.

Best,
Tee

2014-06-29 17:52 GMT-07:00 Jason Swails <jason.swails.gmail.com>:

> On Sat, Jun 28, 2014 at 8:50 PM, Teerapong Pirojsirikul <tpirojsi.ucsd.edu
> >
> wrote:
>
> > Dear AMBER users,
> >
> > I am wondering whether QMMM NEB calculation in AMBER can be applied to
> the
> > study of a reaction pathway associated with bond breaking/forming. As I
> > understand, for this kind of reaction, we would end up with 2 completely
> > different molecules (end points) and this means there would be 2
> different
> > topology files containing structural data for each of them. However, as
> > documented in AMBER tutorial, it seems that 2 end points are required to
> > share the same topology file. Does this mean we cannot use NEB
> calculation
> > with the bond forming/breaking type of reaction?
> >
>
> ‚ÄčA couple comments here.
>
> 1) When you are running a QM/MM calculation, all classical MM terms (bonds,
> angles, torsions, charges, and vdW parameters) between two atoms in the QM
> region are ignored. Therefore, as long as you never try and simulate the
> product state with the reactant state topology file using only a MM
> potential, there should be no problems using the same prmtop for all NEB
> beads.
>
> 2) I believe the only hard requirement for NEB is that all beads have
> exactly the same number of atoms in exactly the same order in every
> topology file.
>
> In any case, (1) is the most important here. If you think about simulating
> a "simple" chemical reaction using QM/MM without using NEB (so you only
> have one 'bead', perhaps using umbrella sampling), the same topology file
> is used to simulate the whole reaction pathway. And that works precisely
> _because_ all MM terms are ignored between QM atoms.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Jun 30 2014 - 11:30:02 PDT
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