- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Jason Swails <jason.swails.gmail.com>

Date: Sun, 29 Jun 2014 20:52:49 -0400

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?
*

*>
*

A 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

Date: Sun, 29 Jun 2014 20:52:49 -0400

On Sat, Jun 28, 2014 at 8:50 PM, Teerapong Pirojsirikul <tpirojsi.ucsd.edu>

wrote:

A 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Jun 29 2014 - 18:00:02 PDT

Custom Search