Questions tagged [computational-chemistry]

For questions about computational chemistry.

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5
votes
0answers
22 views

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

I have tried running a NEB-TS calculation in orca with %pal nprocs 32, but I get an error saying ...
4
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0answers
28 views

What are the challenges in using DFT to study the Hydrogen Evolution Reaction of (111), (110), (100) and (011) planes of Cobalt (III) Phosphide (CoP)

What are the challenges in using DFT (implemented in the VASP code) to study the hydrogen evolution reaction (HER) of the (111), (110), (100) and (011) surface planes of Cobalt (III) Phosphide CoP
18
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9answers
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 ...
8
votes
1answer
122 views

The correlation energy from frozen natural orbtials (FNOs) using CCSD and MPBT(2)?

In other works and from the paper: Scaling Up Electronic Structure Calculations on Quantum Computers: The Frozen Natural Orbital Based Method of Increments. I have seen that the corrected CCSD ...
10
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2answers
122 views

How to convert SMILES to Amino Acids sequence using RDKit

I have the following SMILES, wrapped in Python RDKit: ...
10
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0answers
78 views

Phase transition in Molecular Dynamics simulations

I am reading the book "Computer Simulations of Liquids" by Allen and Tildesley, 2nd edition where on multiple occasions it says MD is valid and has no problem as long as the conditions ...
17
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3answers
1k views

Why is uncertainty not a big problem in computational chemistry?

The molecular Hamiltonian (or, for simplicity, the Fock operator) contains coulomb potentials as well as momentum operators. To evaluate the coulomb potential, we need to know where the electrons are. ...
8
votes
1answer
55 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 ...
7
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2answers
100 views

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

A specific HESSIAN calculation carried out with GAMESS software presents this result: ...
7
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1answer
121 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'...
6
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0answers
31 views

Confused by NBO output, due to missing bonds [closed]

I'm about to do an NBO analysis to evaluate bond characteristics in a novel transition-metal complex. As I have never done anything like that, I tried to understand the basic output for an octahedral ...
6
votes
1answer
53 views

NBO Calculation failing (ATDIAG DISCRD)

I'm trying to perform NBO calculations on a bimetallic complex to evaluate bond orders. However, while I've previously done NBO calculations to obtain partial charges which worked without problems, ...
8
votes
2answers
136 views

Why are method developments and new implementations not done much in Gaussian?

While I have seen many papers in which Gaussian is used in calculations, I have not seen any paper in recent times where new methods are implemented in Gaussian. The latest paper I could find ...
5
votes
1answer
47 views

Change in RDKit's encoding of InChi?

Using RDKit (2020.09.5) I would like to assign InChi to molecules expressed as SMILES and fail to replicate this GitHub gist for initial training written about 2 years ago (RDKit 2019.03.2). I would ...
8
votes
0answers
58 views

Visualizing wavefunctions in real space [closed]

I would like to generate wavefunctions as functions of spatial coordinates (X, Y, Z) using Gaussian G09 and then visualize them. How might I go about doing this? I am using Linux and my preferred ...
6
votes
0answers
69 views

Two-stage unbinding & binding energies with DFT

I'm trying to calculate the stability of the product of a coordinate bonding process of molecules A and B in the polarizable continuum solvent model (PCM, solvent set to water). I'm getting energies ...
5
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0answers
58 views

How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files?

The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
12
votes
1answer
94 views

How can one computationally determine the flammability of a molecular system?

I can imagine one aspect of flammability (the ability of a substance to ignite on fire) to include calculating the kinetics and thermodynamics of the reaction of the system with oxygen. This is not ...
9
votes
1answer
115 views

Understanding emission spectra using TDDFT calculation

I did a TDDFT calculation to get the emission spectra of my molecule. Here are the first five roots for the emission calculation: ...
5
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0answers
105 views

What is the relation between enthalpy, ionization potential, internal energy and HOMO/LUMO?

Is there any relation between enthalpy, ionization potential, internal energy and HOMO/LUMO? I am dehydrogenating a molecule and I need to study the enthalpy of dehydrogenation. If I get any relation ...
7
votes
1answer
136 views

How to extract transition density cube from .fch file in Gaussian?

I have been trying to extract the transition density cube of a simple molecule, $\ce{H_2O}$. I did a regular geometry optimization and then TD-DFT calculation with a keyword ...
8
votes
1answer
115 views

Difference between original STO-3G and BSE STO-3G

I am trying to work with the STO-3G basis set, but I noticed that the STO-3G in Basis set exchange is different from the STO-3G originally published, and not only that, the BSE version seem to be ...
13
votes
2answers
166 views

Analytic Hessians for meta-GGA functionals

In many of the free/open-source QM programs like GAMESS, ORCA, NWChem, the calculation of analytic hessians is not possible when a meta-GGA density functional is used, like M06-2X. My first question ...
6
votes
1answer
170 views

Calculate number of electrons per shell for an atom

Suppose you are given the atomic number of an element, e.g. Technetium, which is 43. Is it possible to return an array which shows the distribution of electrons across different shells of an atom ...
8
votes
1answer
77 views

Excited states using ORMAS flag in GAMESS

I am trying to calculate the excited states using single reference CISD on $\ce{CH3OH},$ using ORMAS' CI-X option in GAMESS. As a test example I am using the $\ce{CH3OH}$ that has 2 core, 7 occ. ...
4
votes
0answers
36 views

Calculating emission spectrum of organic compounds by DFT. Can someone elaborate in terms of calculating it for aggregatrion induced emission? [closed]

I am planning for the calculation of emission spectra of organic compounds showing the phenomenon of aggregation-induced emission (AIE). Can someone help me get started?
11
votes
1answer
263 views

What units are used in Gaussian 16 for dipole derivatives output?

I ran a frequency analysis employing Gaussian 16 on MP2/6-31+G(d,p) level of theory with the keyword iop(7/33=1) in order to have access to dipole derivatives with ...
25
votes
3answers
1k views

What does B3LYP do well? What does it do badly?

I have seen a general criticism of B3LYP in computational chemistry (especially with the 6-31G* basis set). I would like to know some of the more/less obvious problems that occur when using it and ...
10
votes
3answers
549 views

Which DFT functional should I use to simulate spectra of pesticides?

I am mainly searching for functionals to calculate spectra of pesticides. I found the benchmark test from Goerigk and Grimme$^1$, but don't understand which of the functionals suits my purpose the ...
8
votes
1answer
70 views

Calculation of dispersion energies for organometallic complexes with Gaussian

I've tried to calculate dispersion energies of some organometallic complexes with the Gaussian software using WB97XD/Gen (...
10
votes
2answers
89 views

How to create a differential spectrum from two simulated spectra, calculated by two different basis sets?

In my bachelor thesis, I compare simulated IR-spectra computed by different basis sets. The simulated spectra from sets like cc-pVTZ and cc-pVQZ are too similar to compare them by plotting them next ...
7
votes
1answer
72 views

What does "Test job not archived" mean?

I am running frequency computation with geom=connectivity in Gaussian. It all converges now but at the very end of the last convergence it says: ...
8
votes
1answer
184 views

Problem obtaining a Raman spectra of a graphene structure

I am trying to obtain the Raman spectra of a graphene structure using Gaussian. I used the input below, but when I did it, I got this error: ...
10
votes
1answer
129 views

How to generate accurate displacements along normal modes?

How can i displace my structure along a particular normal mode, without coupling to other modes ? Rather than a exact mathematical procedure, I am more interested in a software/script/package that can ...
11
votes
2answers
65 views

What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?

I need to simulate a salt diluted in a liquid electrolyte. My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward. Now I have ...
6
votes
1answer
56 views

Vibrational frequency analysis for NEB result through Maestro

I have ran a Nudged Elastic Band (NEB) calculation using QuantumEspresso through Maestro to find the potential transition state. Within Maestro there is an option where you can select for NEB type ...
10
votes
1answer
141 views

Computing optimized 3D structures in python that take solvent into account

I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows: ...
13
votes
2answers
329 views

How to get potential energy surface from GAMESS?

I'm trying to learn GAMESS and performing a simple PES scan of oxygen molecule. After the completion of the calculations I get a .log file with lots of sections like that: ...
10
votes
1answer
148 views

What novel drugs are developed via CADD?

Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery. Which drugs that have ...
12
votes
1answer
82 views

Excited state energy gradient during geometry optimization of a target excited state

During the geometry optimization of the ground state of a molecule, we try to optimize the energy gradient with respect to the nuclear positions such that the system remains in its lowest energy state....
8
votes
1answer
540 views

Formation energy and Energy above convex hull as indicators of stability

I was trying to understand some indicators about the stability of materials (that basically tell you whether it can be synthesized or not.. right?). Specifically, I'm trying to link the knowledge of ...
23
votes
2answers
898 views

Why do people care about reversibility in molecular dynamics simulations?

When carrying out a molecular dynamics simulation, one has to choose an ensemble. Depending on the problem, one usually works in the microcanonical (NVE), canonical (NVT), or grand canonical ensemble (...
7
votes
1answer
37 views

The number of long-range interaction pairs in Tinker

I tested MM calculation of a benzene molecule with Tinker. The following is the xyz file used for the input. ...
13
votes
1answer
138 views

Are nuclear ab-initio methods related to materials ab-initio methods?

I just read this synopsis in Physics where scientists used first-principles nuclear physics calculations to predict the stability of 700 isotopes up to iron. I didn't know that this was possible, ...
9
votes
1answer
119 views

Error running psi4 on charged molecules

I am running a simple energy calculation on a conformer of 3-Sulfopropyl methacrylate, which is given my C=C(C)C(=O)OCCCS(=O)(=O)[O-]. This is my workflow: ...
9
votes
1answer
405 views

Using OpenBabel or RDKIT Python API to generate conformers from a SMILES string

I have a bunch of monomers in the form of SMILES string and I want to generate conformers from them. At the moment, I am using RDKit to convert these SMILES strings to .sdf files, then using ...
12
votes
1answer
209 views

How to get more significant digits from OpenBabel?

I am generating conformers from SMILES string using OpenBabel. The shell script looks something like: ...
8
votes
2answers
256 views

How do I figure out how many monomer configurations I need for my simulation?

I am running a quantum mechanical simulation on Psi4 for a certain number of monomers to generate data for a database. Some of these monomers are short, while some are long. At the moment, I am ...
10
votes
1answer
148 views

Calculating/Visualizing electronic density from orbital information written in the Molden format

I'm trying to obtain an electron density from orbital information written in the Molden format by the formula, $$ \rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. \tag{1} $$ Is there any ...
9
votes
3answers
394 views

What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?

I would like to construct a model analytical potential function for collision between CH3Cl and Ar. This would be the sum of CH3Cl intramolecular + CH3Cl---Ar intermolecular potential. First I would ...