Skip to main content
6 votes

A good 2D function for plotting and visual demonstration of transition state, reaction coordinate etc

EDIT: Turns out it can be extremely simple to do. Here are the ingredients: Component Expression Curved minimum energy path (path follows $y = 0.4 (x^2 - 4x)$) $[y - 0.4(x^2-4x)]^2$ Ridge (runs ...
Shern Ren Tee's user avatar
6 votes

A good 2D function for plotting and visual demonstration of transition state, reaction coordinate etc

I would suggest using the egg holder function which is defined by the following formula $ f(x) = -(x_2+47)sin\left(\sqrt{\left| x_2+\frac{x_1}{2} + 47 \right|}\right) - x_1sin\left(\sqrt{\left| x_1-(...
Hemanth Haridas's user avatar
5 votes
Accepted

Gaussian 16: Relaxed scan using Jacobi coordinates expressed using generalized internal coordinates

Based on the GIC page in Gaussian website and your picture, the definition of the coordinates would be: ...
S R Maiti's user avatar
  • 7,011
5 votes

Do conformations arise from vibrations?

Yes, you can think of conformations as arising from vibrational modes, typically low-energy ones. In fact, some conformational search methods use low-energy dynamics or projection to find new ...
Geoff Hutchison's user avatar
4 votes
Accepted

What is the gold standard ab initio pair-potential between two water molecules?

I'm not an expert, but I believe Paesani's many-body MBPol force fields Acc. Chem. Res. 49, 1844 (2016) afford some of the most accurate descriptions of the interactions between water molecules. The ...
Susi Lehtola's user avatar
  • 19.7k
4 votes

Using Hindered Rotor Scans With Different Convergence Criteria from Gaussian

That’s a bit up to interpretation… I guess it depends on what you want to get out of the scans exactly (i.e., are the geometries important, or just the energies on those geometries?). If you want the ...
isolated matrix's user avatar
4 votes
Accepted

What is the branching space of a conical section?

A paper called "Potential energy surfaces near intersections" [1] provides the answer. At the conical intersection, the energies of two potential energy surfaces parameterized by ...
elutionary's user avatar
4 votes

Script to draw one-dimensional PES comparing harmonic and anharmonic vibrational modes

A script that works for arbitrary potentials My script has produced the following figures for this paper. Simple single-well potential: Double-minimum potential with a small barrier and a "shelf&...
Nike Dattani - No Free Time's user avatar
3 votes

How do I do a PES (potential energy surface) scan for the excited electronic state?

To scan the potential energy surface (PES) for an excited electronic state, you can do the same thing that you would do for scanning the PES for the ground electronic state, except that you need to ...
Nike Dattani - No Free Time's user avatar
2 votes

What is the branching space of a conical section?

I'm a bit late to the party but if you're interested I can provide some further information. In general the PES(in the Born Oppenheimer approximation) has dimensionality 3N-6, where N is defined to be ...
mathbruh67's user avatar
2 votes

Gaussian 16: Relaxed scan using Jacobi coordinates expressed using generalized internal coordinates

Defining the geometry in terms of z-matrix internal coordinates would make this very easy, I think. Define COM as a dummy atom, place another dummy atom to define the molecular plane, place A and B ...
Frank Jensen's user avatar
  • 1,776
1 vote
Accepted

Si Thin film phonon dispersion with negative frequency

Just because the structure is simple with high symmetry doesn't mean it's the correct ground state. More often that not, symmetry breaking leads to interesting physics (e.g. the surface reconstruction ...
Tyler Sterling's user avatar
1 vote

Potential Energy curve for CO2 and a surface

The most likely culprit is using tail yes. That adds a correction energy which theoretically accounts for the truncation of the LJ parameter, but is only designed ...
Shern Ren Tee's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible