Questions tagged [computational-chemistry]
For questions about computational chemistry.
104
questions
4
votes
0answers
11 views
Is there a way to set different special bonds for different atom groups in the same structure in LAMMPS?
I am running some simulations on a metal organic framework and I need to set different 1-4 coul and lj parameters for different ...
8
votes
2answers
637 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 ...
5
votes
0answers
17 views
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 that one must have an executable file ...
8
votes
2answers
210 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 ...
10
votes
3answers
234 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 ...
5
votes
1answer
113 views
Unrecognized or duplicated keyword error using ORCA
I wanted to run ORCA 5.0.2 with the following input:
...
5
votes
0answers
33 views
Segmentation fault during execution of Orca 4.0.0.1
I would like to use Orca 4.0.0.1 under the following Linux version:
...
7
votes
1answer
259 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 ...
9
votes
1answer
62 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 ...
11
votes
2answers
405 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 ...
6
votes
0answers
47 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
votes
0answers
45 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.
20
votes
10answers
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 ...
12
votes
2answers
197 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 ...
10
votes
2answers
143 views
How to convert SMILES to Amino Acids sequence using RDKit
I have the following SMILES, wrapped in Python RDKit:
...
10
votes
1answer
110 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 ...
9
votes
1answer
56 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 ...
8
votes
1answer
156 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'...
8
votes
2answers
105 views
Vibrational frequencies results with GAMESS. Is it an equilibrium geometry?
A specific HESSIAN calculation carried out with GAMESS software presents this result:
...
5
votes
0answers
74 views
Methods to study reaction mechanisms in solid state reactions and identifying intermediates
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 ...
6
votes
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 ...
11
votes
0answers
118 views
How may I calculate the "effective transfer integral" in free electronic-structure software?
I would like to calculate the following four quantities in a free electronic structure program:
\begin{alignat}{2}\tag{1}
e_1&=\langle\phi_1|H^{KS}|\phi_1\rangle,\\
e_2&=\langle\phi_2|H^{KS}|\...
6
votes
1answer
55 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, ...
5
votes
1answer
52 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
2answers
140 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 ...
8
votes
0answers
59 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 ...
5
votes
0answers
73 views
How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files? [closed]
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 ...
8
votes
1answer
118 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 ...
7
votes
1answer
159 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 ...
6
votes
1answer
173 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 ...
17
votes
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. ...
4
votes
0answers
39 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
296 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 ...
8
votes
1answer
82 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. ...
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
73 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 (...
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
2answers
91 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 ...
8
votes
1answer
189 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:
...
7
votes
1answer
78 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:
...
10
votes
1answer
130 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
71 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
65 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
159 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:
...
10
votes
1answer
149 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
90 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....
6
votes
0answers
90 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 ...
9
votes
1answer
129 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:
...
8
votes
1answer
661 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 ...
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.
...
