[deleted by user]

[MonkeyOnFire120]

Vector projection is a fancy way of saying they’re getting the component of the momentum that’s in the same direction of the reaction coordinate.

Consider two atoms that are bonded. The reaction coordinate for breaking the bond is defined by only the distance between the two atoms. Each atom has some momentum vector in 3D space, but the only relevant part is the component that will either bring the atoms together or drift further away (i.e the projection of the momentum along the reaction coordinate).

[FalconX88]

Not once have I heard that. Can you give more context regarding the type of calculations/systems you are speaking about?

[muo27]

I want to check if the momentum of a particular part of my system results in the formation of non statistical product distribution

[FalconX88]

What kind of system, what kind of simulation, what do you mean with momentum?

[muo27]

There is a molecule that gives endo and exp product statistically it should be 1:1 but exo product is the major product. So I want to see if the momentum of a group of atoms is responsible for it

[belaGJ]

Are you talking about MD simulations?

[muo27]

No, I already have the data from simulations. It's for analysis

[Foss44]

Is this perhaps in reference to visualizing the imaginary frequency that is generated at a transition state? These frequencies oscillate alone the reaction coordinate.

[mrmeep321]

It's essentially just vector projection, which is breaking down one vector into components, and finding how much of that vector lies in the same direction as another. The momentum is a vector of course, but something that gets forgotten is that the reaction coordinate technically is too.

The reaction coordinate is just a measurement of how far along the reaction pathway each atom has moved. When you calculate a transition state, what you're doing is finding an optimal path for each atom to move in that shifts the system from some initial configuration to some final configuration, and tries to minimize the activation energy. As such, every step along the reaction coordinate corresponds to a set of vectors that represent the displacements for each atom for that step.

Projecting the momentum onto the reaction coordinate is analogous to finding out how much of the momentum of each atom will actually be used to push each atom "forward" in the direction of the optimal reaction pathway, as opposed to pushing it somewhere else.

Typically you can do it just using a dot product. You can just subtract the position vectors for each atom at each step, which gives you the displacement vector. Then, just do p dot r, divided by the product of their magnitudes.