Questions tagged [computational-chemistry]
For questions about computational chemistry.
70
questions
11
votes
1answer
121 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 ...
7
votes
0answers
50 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
538 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
60 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 (...
24
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
82 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
173 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
35 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
122 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
61 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
41 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
107 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
143 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
63 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
56 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
votes
0answers
53 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:
...
7
votes
1answer
137 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
34 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
132 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, ...
5
votes
0answers
73 views
What is the relation between enthalpy, ionisation potential, internal energy and HOMO/LUMO?
Is there any relation between enthalpy, ionisation 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 ...
8
votes
1answer
65 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:
...
11
votes
1answer
190 views
How to get more significant digits from OpenBabel?
I am generating conformers from SMILES string using OpenBabel.
The shell script looks something like:
...
9
votes
1answer
152 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 ...
8
votes
2answers
251 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
137 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
375 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 ...
9
votes
2answers
224 views
What are Pair Natural Orbitals?
Recently, I came across electron correlation methods that use local pair natural orbitals (LPNOs) or domain-based local pair natural orbitals (DLPNO), such as DLPNO-MP2, DLPNO-CCSD etc. The dynamic ...
9
votes
1answer
88 views
Energy cut-off value for conformer calculations
I want to get familiar with the conformer calculation. I found a paper where they did the conformer calculations already for the molecule I work with. The paper can found here.
In the experimental ...
8
votes
1answer
44 views
Simulation of electronic potential from nanoparticles interacting with molecules
I work with SERS, where the Raman signal gets enhanced by the electric field of the nanoparticles. Now I like to simulate this kind of spectrum with Gaussian. I found a paper[1], where it looks very ...
11
votes
1answer
224 views
What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?
What are some of the biggest open-questions / challenges in Condensed Phase theory and computation? What efforts are being done to answer them?
I realize Condensed Phase chemistry is a huge field, but ...
6
votes
1answer
339 views
How to choose starting magnetization while doing spin polarised calculation in Quantum ESPRESSO?
I am trying to run spin polarised DFT calculation in Quantum ESPRESSO on system Co2MnSi. I kept starting magnetization for all these three species as,
...
10
votes
1answer
117 views
What are the trade-offs setting DIRSCF to either .TRUE. or .FALSE. (the default) in GAMESS (US)?
The first software I used to run calculations was Gaussian09. When submitting a input, I used to see a pattern of resource usage where the allocated CPU quickly maxed out, remaining high most of the ...
8
votes
1answer
150 views
Which basis set should be used for a system that contains both anions and cations?
I am trying to model a system that has both anions and cations interacting with each other. (In this case it is calcium ion interacting with two small carboxylic acid molecules). Now, looking through ...
11
votes
0answers
73 views
Bioisosteric replacement using SMARTS (KNIME and RDKit) [closed]
I am trying to create a KNIME workflow that would accept a list of compounds and carry out bioisosteric replacements (we will use the following example here: carboxylic acid to tetrazole) ...
15
votes
2answers
103 views
What is the difference between orbital localisation and NBO?
I am new to computational chemistry, I have used mainly GAMESS and Orca. In GAMESS, there are orbital localisation schemes like Pipek-Mezey, Ruedenberg-Edminston, etc. which generate orbitals that ...
13
votes
2answers
263 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:
...
7
votes
1answer
674 views
What is the physical meaning of occupations='smearing' in Quantum ESPRESSO?
I want to understand, what is the intuition behind using the occupations='smearing' or 'tetrahedra' in Quantum ESPRESSO input file? I mean how we can interpret what is going to happen inside of ...
9
votes
1answer
394 views
How to do spin polarization calculations using Quantum ESPRESSO?
I am currently new to DFT calculations in Quantum ESPRESSO. Though, I have read some research papers for determining spin polarization and Half-metallicity in certain Heusler alloys. These research ...
11
votes
1answer
127 views
Predicting magnetic moment of a metal complex computationally
Recently, for entrance exams, I have been dealing with a lot of weird compounds. One of them is $\ce{K3[Mn(CN)6]}$.
The objective was to predict the magnetic moment of the above complex.
I predict ...
9
votes
2answers
432 views
How to choose pseudopotential for DFT calculations in Quantum ESPRESSO?
I am a beginner and newly started running DFT calculations to find out the electronic band structure of certain materials in Quantum ESPRESSO. But we have to select the pseudopotential for running the ...
10
votes
0answers
96 views
I have access to 1000 cores across 10 nodes, what would be the best way to prallelize an MP2, GW, or RPA calculation for a periodic system in VASP? [closed]
What's the best way for parallelization in VASP for periodic systems? In the documentation, it mostly explains it for the local computer and molecule calculation. Apparently, these explanations don't ...
9
votes
1answer
386 views
High precision helium energy
In the paper "High Precision Theory of Atomic Helium", Drake lists the then best-known ground state energy of the Schrödinger equation for helium to 22 digits as:
$$\lambda_0 \approx -2....
9
votes
1answer
42 views
How can I determine the maximum value of a spin orbital and its derivative in any direction?
I'd like to be able to recover the maximum value that any of the basis functions can take, as well as their maximum derivative. How can I do this?
For context, I need it because I want to calculate ...
10
votes
2answers
89 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 ...
8
votes
1answer
116 views
Are there other custom chemistry programming languages besides SVL?
I must confess some ignorance... I just became aware of the Scientific Vector Language (SVL) which has been around since 1994 and was created solely for computational chemistry.
It has a large ...
10
votes
1answer
92 views
Correcting thermodynamic data for concentration, what concentration is best to use?
In computational chemistry when using transition state theory we often use standard states for all involved structures. However, sometimes people argue that it should be corrected for concentration (...
21
votes
2answers
809 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 (...
8
votes
0answers
68 views
Equilibration of normal modes in water molecule [closed]
When running a molecular dynamics simulation on a singular water molecule in vacuum to analyze its normal modes of vibration from the NVE (microcanonical) ensemble, the bending mode frequency is ...
8
votes
1answer
325 views
How to perform virtual crystal approximation calculations in VASP?
Can someone share appropriate tags and methods to perform virtual crystal approximation calculations in VASP?
8
votes
1answer
1k views
How to fix Error Link9999 in Gaussian
I have a problem with geometry optimization in Gaussian software with M062X method. The structure was smoothly optimized using M062X/Gen. Nevertheless, I need very accurate results so afterwards the ...
