Questions tagged [computational-chemistry]

For questions about computational chemistry.

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How to define a chemical bond computationally?

I'm working with an amorphous system. With oxygen, my system has both covalent and ionic bond forming cations. I utilise the Wannier centre approach to define a covalent bond, and my theory is that if ...
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3 votes
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What is the difference between NBO program and NBO that we find in Gaussian?

I'm a little bit lost with NBO (natural bond orbital) analysis in Gaussian. I was told that pop=NBO in Gaussian gives me the charges of atoms, but that the NBO ...
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error termination while performing NTO analysis in G09?

I'm trying to perform an NTO analysis (Natural transition orbitals) for my system. I first used TDDFT to calculate the excited states and then generated my chk file and copied it under the name of ...
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  • 141
5 votes
1 answer
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How can I distinguish between n, pi, pi* orbitals when looking for excited states?

I recently asked about how to distinguish between transition types. I got an answer there about determining the character or type of the orbitals. My problem now is that I'm not sure how to determine ...
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how can I distiguish between pi-pi* or n-pi* while doing a TDDFT calculus on gaussian?

Hi I have a system that belongs to the C1 point group which is polycyclic and contains heteroatomes ,when calculating the excited states by TDDFT and after visualising the MOs that are envolved on ...
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  • 141
4 votes
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80 views

ORCA finished by error termination in SCF gradient

I try to optimize and compute frequencies for the system built up from C, O, H, and Co atoms in the following functionals: B2PLYP, B2PLYP-D3, B3LYP, B3LYP-D3, BLYP, BLYP-D3, DSD-PBEP86, PBE, PBE-D3, ...
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6 votes
1 answer
96 views

How exactly are valence orbitals combined in split valence basis sets such as 3-21G?

For hydrogen, the 3-21G basis set (in CFOUR format) is ...
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4 votes
0 answers
26 views

Radius of gyration and aggregates

I have performed a MD simulation using GROMACS for a system of 100 caffeine molecules in water. It is expected caffeine form aggregates. I have calculated the radius of gyration for the simulation ...
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3 votes
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Calculating the Diffusion coffecients from Trajectory file in ASE

I plan to study the Diffusion-Coefficient of my simulation outputs, for this, I want to use ASE. Sadly I am not entirely sure of how to proceed, has anyone done this and if yes, please share your ...
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4 votes
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Benchmarks for optimised Math Libraries across platforms

Are there any benchmarks of low-level and high-level math operations from different Math libraries on corresponding architectures? Here are a few packages: LAPACK / BLAS + ATLAS (stock version from ...
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5 votes
0 answers
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How to run SCRF in Gaussian with extra basis?

I want to run a SCRF calculation in Gaussian for a molecule. This has been done as standard with several geometries without issue using the aug-cc-pvtz basis and ...
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14 votes
2 answers
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Textbooks for electronic structure theory

Through this post I am looking to create a resourceful list of textbooks for any one interested in electronic structure theory. The focus here is to create mostly a mutually exclusive list of answers ...
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8 votes
2 answers
207 views

What does it mean when the first order correction energy is 0?

Suppose I have the following Hamiltonian to start $$ H_0 = \begin{pmatrix} 0 & 0 & 0 & 0\\ 0 & 0 & 2 & 0\\ 0 & 2 & 0 & 0\\ 0 & 0 & 0 & 0 \end{pmatrix} $$...
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Error: hangup in Gaussian 09

I have the following problem to run a calculation using Gaussian 9. The calculation starts running and after a few hours stop. The nohup file has the following ...
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3 votes
0 answers
72 views

Atomic Simulation Environment (ASE) is unable to read a big trajectory file

The problem that I face is the ASE software can't read the trajectory file and throws this error ValueError: buffer is smaller than requested size. My assumption is ...
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5 votes
1 answer
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How do you determine substitution patterns using RDKit?

So I have a list of molecules. They all have a common substructure, but different substitution patterns. For example, in the figure below, the leftmost molecule is the base, and the center and ...
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3 votes
0 answers
45 views

How can we test the force field (parameter) for a complex?

I built a force field for a complex. How can I check if the force field is working well or no? I did a short molecular dynamics using AMBER only for the complex using the parameters I built. It worked ...
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2 votes
0 answers
74 views

Rashba effect and VASP

How to prove by first-principles DFT calculations that the compound has Strong spin-orbit coupling and Rashba effect
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  • 495
6 votes
2 answers
381 views

Parameterising a Lennard-Jones interaction: Which atoms should I scan to build potential energy surface?

I have a question related to parameterize Lennard-Jones interaction to get sigma $\sigma$ and epsilon $\epsilon$ to include in amber force field to do the Molecular Dynamics. I searched a lot, they ...
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2 votes
0 answers
19 views

Building a script to automatically save .xyz format files from geometry optimization with AMMP in VegaZZ

I'm totally new to programming and computational chemistry. I'm using Vega ZZ as a free software to compute geometry optimization via MM (AMMP) in order to optimize the geometry of the found minima ...
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5 votes
0 answers
36 views

Getting Internal Calculator Data in ASE

I am using the framework ASE to do computational chemistry calculations. I am using the calculator GPAW with it. How do I extract data that is internal to the calculator? I mostly want to get the ...
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6 votes
2 answers
104 views

Convert ase atoms to pymatgen structure

I have atom_row from ase_db. I have tried various methods but they all fail. Seems like I'm missing a lattice, but I don't know what that is and where I can get it ...
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6 votes
1 answer
111 views

Transforming from CI basis to MO basis

Suppose, one knows the ground state wave function $|\Phi\rangle$ in terms of a slater determinant(SD) basis say, from a Configuration interaction calculation. $$|\Phi\rangle= c_{\text{HF}}\left|\Psi_{\...
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7 votes
1 answer
124 views

Hartree-Fock Method: Projection of density matrix onto a larger basis set

I am implementing a Hartree-Fock SCF program with an educational purpose. Although the code works fine using a Core Hamiltonian guess for the SCF iterative process, I want to implement a more accurate ...
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14 votes
3 answers
1k views

Can DFT simulate chemical reactions?

I was wondering, can you simulate the chemical reaction between two or more molecules using DFT? If not, what numerical method is usually used for this?
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14 votes
1 answer
641 views

How to start a Machine Learning project for chemical properties prediction?

I know that is a very general question but I would like to start a ML project in Python to predict some chemical properties with a large set of experimental data. The compounds I would like to study ...
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10 votes
1 answer
91 views

Correlation tables between irreps for f orbitals

I want to define occupied orbitals in terms of IRREPs for tungsten which has f orbitals. The highest possible point group for $\ce{WF2}$ in MOLPRO is $D_{2\mathrm h}...
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6 votes
0 answers
91 views

How to calculate circular dichroism in VASP?

Is there an option to calculate circular dichroism (CD spectra) and anisotropic Dissymmetry factor in VASP. I need to calculate the spectra for chiral system
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7 votes
1 answer
127 views

Is It possible to do microkinetic modelling for liquid phase reactions, in the presence of a catalyst?

As from the title, I want to do NEB-TS for chemical reactions in the liquid phase, and use the information to calculate reaction rates/kinetic rates. I know that the NEB-TS is possible in the liquid ...
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7 votes
0 answers
53 views

Can Markov State Models based on short-term non-equilibrium datasets also capture the dynamics towards equilibrium?

I am non-specialist who is new to the field of computational physics/biology. I have a few questions about the relevance and effectiveness of Markov State Models (MSM) in capturing the dynamics ...
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5 votes
1 answer
138 views

Convert a POSCAR-format-like file to a XSF file?

How do I convert a POSCAR-format-like file to a XSF file (visualized by XCrySDen)? I'm looking for a step by step tutorial on the process and what tools/programs are needed.
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5 votes
0 answers
33 views

Is there a way to set different special bonds for different atom groups in the same structure in LAMMPS? [closed]

I am running some simulations on a metal organic framework and I need to set different 1-4 coul and lj parameters for different ...
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8 votes
2 answers
659 views

Is there a benchmark paper that takes into account how often each molecule is studied?

There are many benchmark sets in different branches of computational chemistry and physics, that are frequently used to assess the "average error" of a method for a certain property, on a ...
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5 votes
0 answers
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Autodock Vina Error on Chimera: Service "local" unavailable

I was confronted with an error, upon trying to dock a minimized ligand to a target protein, that the "service 'local' [is] unavailable". I then realized ...
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9 votes
2 answers
477 views

Which methods are size-consistent / size-extensive, and why?

This is a follow up question from another question I posted here. I am looking for an explanation (or a mathematical proof, if possible) of the size extensivity and size consistency of the following ...
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10 votes
3 answers
320 views

How to plot molecules with angles and bond lengths

There are many programs out there where you pass an XYZ coordinate file and the program will give you a visualization of the molecule. I want to make a plot like the one in the picture, with bond ...
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5 votes
1 answer
244 views

Unrecognized or duplicated keyword error using ORCA

I wanted to run ORCA 5.0.2 with the following input: ...
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  • 343
7 votes
1 answer
314 views

Where to find organic molecules atomic coordinates

I have found many organic molecule databases, such as PubChem or chEMBL. But they don't provide the atomic coordinates of each atom on the structure. I'm especially interested in organic molecules ...
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9 votes
1 answer
68 views

Which molecules have multi-reference character?

I'm using WebMO to construct molecules that have high multireference character, but I cannot seem to find any, or perhaps I'm not building them correctly on WebMO; I know singlet biradicals generally ...
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11 votes
2 answers
418 views

Where to find DNA structural atomic coordinates?

I need a code/app/website that can receive a DNA sequence, for instance AATCT, and output a file with the atomic coordinates. I used to do this on this website but the service is no longer working and ...
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6 votes
0 answers
124 views

How do you perform parallelization of NEB-TS in ORCA? [closed]

I have tried running a NEB-TS calculation in orca with %pal nprocs 32, but I get an error saying ...
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5 votes
1 answer
122 views

Using DFT to study Hydrogen Evolution Reaction on a surface?

How well can DFT, as implemented in VASP, describe surface reactions? For example, I want to study the hydrogen evolution reaction (HER) on the $(111), (110), (100) \text{ and } (011)$ surface planes ...
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20 votes
10 answers
4k views

GUIs for Quantum Chemistry... Where are they?

I have a general and maybe a little silly / funny question. Why don't most CompChem or QuantumChem software have a GUI? SIESTA is trying with Simune as far as I know, but even proprietary software ...
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12 votes
2 answers
249 views

Phase transition in Molecular Dynamics simulations

I am reading the book Computer Simulation of Liquids[1] where on multiple occasions it says MD is valid as long as the conditions simulated are away from phase transition. For example, at the ...
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10 votes
2 answers
297 views

How to convert SMILES to Amino Acids sequence using RDKit

I have the following SMILES, wrapped in Python RDKit: ...
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10 votes
1 answer
134 views

Can electron-phonon coupling be extracted from the dielectric function?

Computationally, there are various ways to calculate the electron-phonon coupling constants as a function of phonon index and momentum. My question is about the reverse process. Let us say that an ...
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9 votes
1 answer
65 views

Is there a standard file format for storing one and two electron integrals?

Is there any standard file format (.txt, .dat etc) for storing one and two electron integrals (generated from ab initio packages) which doesn't compromise on precision and is convenient for reading ...
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8 votes
1 answer
271 views

How to generate a input file for gaussian in Avogadro 2? [duplicate]

I made auto optimization working by installing openbabel using sudo apt install openbabel. Is there any way to make Gaussian extension working by doing something? I'...
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  • 81
8 votes
2 answers
146 views

Vibrational frequencies results with GAMESS. Is it an equilibrium geometry?

A specific HESSIAN calculation carried out with GAMESS software presents this result: ...
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  • 81
5 votes
0 answers
79 views

Methods to study reaction mechanisms in solid state reactions and identifying intermediates [closed]

An example of a solid state reaction: sintering of an initial powder of reactants leading to a product. Densification of the sintered powder giving a highly pure product powder. What methods (ab ...
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