14 votes
Accepted

How can I specify different theory levels for different atoms in Gaussian?

While ONIOM QM/QM is possible, I don't think that is what you want to be doing. From your example input, it looks like you are just trying to use a different basis function on specific atoms, but the ...
Tyberius's user avatar
  • 15.5k
7 votes
Accepted

Use of genetic algorithm based methods for geometry optimization

The paper you cite has certainly left a legacy, but it is by now almost 30 years old! I think its main insight is in applying physics-agnostic, information-theoretic ideas to atomistic coordinates. (...
Shern Ren Tee's user avatar
7 votes

Number of k-points for unit and super cell

Why is plane wave basis set is good for 1s and 2s orbitals, but for higher convergence is poor? I guess by "higher" you mean higher principle quantum number $n$ (i.e., 3s, 4s-orbitals). For ...
Chengcheng Xiao's user avatar
7 votes
Accepted

Geometry optimization: nuclear coordinates vs lattice parameters

Minimizing energy with respect to nuclear coordinates and with respect to lattice parameters are two very different things. Minimizing energy with respect to nuclear coordinates can be used for ...
Camps's user avatar
  • 23.3k
7 votes

How many non-redundant internal coordinates are needed for optimisation of linear molecule?

Indeed, Baker's delocalized coordinates routines generate 3N-6 (or 3N-5 for linear molecules) coordinates automagically. Note our small contribution where we distinguish between strong and weak ...
MSwart's user avatar
  • 1,064
6 votes

MOPAC: Is there a simple way to display geometry trajectories

I created a Python script to manipulate the MOPAC output, saving a XYZ file with all the structures from the optimization step. Then, the XYZ can be loaded into Jmol software and do the animation. The ...
Camps's user avatar
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6 votes

DFT calculation for conjugated polymers

Apologies I do not have enough reputation points to post this as a comment. You might have already considered other electronic structure methods, but I would like to suggest consider using density ...
squareroottwo's user avatar
6 votes
Accepted

Convergence problem in geometry optimization in Gaussian16

As Camps mentions in the comments, a common approach for improving geometry convergence is to start with less accurate method/basis or use lower precision convergence criteria and incrementally build ...
Tyberius's user avatar
  • 15.5k
5 votes

Is it okay to use semi-empirical methods to optimize structures if I perform high-level energy calculations?

I generally try to use the most accurate methods that my resources will allow me to use, within a reasonable budget for the desired accuracy. If you're interested in 20 water molecules or 60 atoms (...
I have no free time anymore's user avatar
4 votes

How to select charge and multiplicity for macro-molecules?

Unless there are transition metals (e.g. Fe, Mn, Cu, Ni) present in the active site, proteins typically have singlet state. There are several programs out there, such as propka, that can propose ...
MSwart's user avatar
  • 1,064
4 votes

How to select charge and multiplicity for macro-molecules?

Sometimes the protein has been studied experimentally (or thoroughly by theory), and a consensus has been made about the most common charge and multiplicity for the molecule. In most cases, I would ...
I have no free time anymore's user avatar
4 votes

Why the relaxation of my material in Quantum ESPRESSO wasn't achieved?

Optimization does not guarantee that you have achieved a well-converged geometry. It only means that the differences in energy, cell-volume and forces calculated between two successive steps are ...
Hemanth Haridas's user avatar
4 votes
Accepted

ORCA crashes because of RI approximation?

What the doc wants to say is that the program may make an automatic choice of the auxiliary basis set (typically def2/J for non-relativistic calculations and SARC/J for relativistic ones, if I'm not ...
wzkchem5's user avatar
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4 votes
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Making Deuterium POTCAR file for optimization in VASP software

Hydrogen and deuterium are basically identical electronically (*) and you should use the same pseudopotential (POTCAR) for each. You should not see any difference between hydrogen and deuterium (or ...
Phil Hasnip's user avatar
  • 7,157
4 votes

Singlet excited state optimization gaussian issue

If you want the excited singlet state, I suggest you only calculate these, and not the 50:50. Optimization with roots higher than 1 is often tricky, and if you only calculate the singlet excited ...
Frank Jensen's user avatar
  • 1,766
4 votes

Large energy differences across successive geometry optimization steps in SIESTA

In order to calculate the adsorption energies of cetophenone on a nickel surface, you need to do three calculations. Considering the same cell parameters: Run a calculation with only the nickel ...
Camps's user avatar
  • 23.3k
4 votes
Accepted

Is it possible to do a vc-relax calculation using GPAW?

This is more of an ASE question, given that a python script using ASE is employed to set up and run the GPAW calculation. GPAW only is used to compute energies/forces/stresses for a given structure, ...
Kristof Bal's user avatar
  • 1,331
3 votes

What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si

First, "best" is ill-defined. The best method would be full configuration interaction at the complete basis set limit including fully relativistic and quantum field theoretical corrections; ...
Susi Lehtola's user avatar
  • 19.1k
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 ...
I have no free time anymore's user avatar
3 votes
Accepted

Computing proton-proton potentials for infinite periodic materials

In electronic structure calculations for infinite periodic materials, the proton-proton energy is typically not directly computed or used to monitor the convergence of the self-consistent field (SCF) ...
Jaafar Mehrez's user avatar
3 votes
Accepted

How to pre-optimize metal-organic complexes in RDKit using UFF?

Okay, there's a bunch to answer here, but I'll do my best. Take a look at the page for Tetraamminecopper(2+) sulfate on pubchem. The SMILES on there is incorrect and no geometry can be generated on ...
Geoff Hutchison's user avatar
2 votes

Choice of coordinate system for geometry optimization

See our paper from 2006 and references therein: IJQC2006. M. Swart and F.M. Bickelhaupt, "Optimization of strong and weak coordinates", Int. J. Quant. Chem. 2006, 106, 2536-2544 In this ...
MSwart's user avatar
  • 1,064
2 votes
Accepted

Is the Broyden's algorithm sufficient to obtain the crystal structure of a hypothetical alloy, or should something else be used?

BFGS is a local minimization method - it will find you the closest minimum to your starting structure - whereas finding the crystal structure is a global optimization problem: what is the structure ...
Susi Lehtola's user avatar
  • 19.1k
2 votes
Accepted

Cannot optimize hexa aqua Cu(II) and Fe(III)

Th geometry at the start in Th point group otherwise its just mangling and cannot smoothly decrease; Optimiazation in z-matrix ...
farmaceut's user avatar
  • 556
2 votes

Cannot optimize hexa aqua Cu(II) and Fe(III)

For my paper from 2008 I started from the coordinates by Pierloot and co-workers. They used C(i) symmetry for their CASPT2 study of Fe(II)(H2O)6, which you might do as well as a starting point. Second,...
MSwart's user avatar
  • 1,064
2 votes
Accepted

UseSym Keyword in ORCA fails to find appropriate number of SALCs

As you said, your initial geometry may be on the verge of satisfying and not satisfying the Cs symmetry under ORCA's default threshold. Also note that although the molecule should eventually reach ...
wzkchem5's user avatar
  • 9,621
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

Why is this geometry optimization in Gaussian not working for a system containing an amino acid, a water molecule and a metal (Pb) ion?

Thanks for updating the question PriZarah, I can now at least suggest what might be causing the problem. It's probably just very, very slow In your recent example, you are calculating a reasonably ...
leeman's user avatar
  • 246
1 vote

Number of k-points for unit and super cell

I will explicit my comment, the use of plane waves (PWs) for 1s and 2s is completely absurd when a linear combination of atomic orbitals gives a fast convergence. Even if they lack of significant ...
M06-2x's user avatar
  • 906

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