Questions tagged [computational-chemistry]

For questions about computational chemistry.

Filter by
Sorted by
Tagged with
27
votes
1answer
595 views

Approximate equivalence table between Pople's basis sets and Jensen's DFT optimized polarization consistent basis sets (pcseg-n)

At first I posted this question in chemistry.stackexchange.com, before materials.stackexchange.com was launched in beta. As it went unaswered, I'm giving a try here. I have some calculations results ...
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 ...
24
votes
2answers
2k views

What are the “smart algorithms” applied to solve the “curse of dimensionality”?

The "curse of dimensionality" is an ubiquitous issue arising in both electronic structure and quantum molecular dynamics, which refers to the exponential scaling of computational cost with ...
21
votes
2answers
811 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 (...
19
votes
3answers
254 views

What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?

I want to make a pet project in cheminformatics and I need to hear from the community about the actual challenges in chemistry that might be resolved with a digital solution. I've been working in ...
17
votes
6answers
321 views

What are the applications of chemical graph theory?

Graph theory was originally introduced in computer science to study data structure. Chemists also introduced graph theory to study the relation between structure and properties for molecular compounds....
16
votes
3answers
437 views

How well can we model chemical synthesis?

The Materials Genome Initiative held a 2017 workshop, that led to this published report: de Pablo et al., "New frontiers for the materials initiative," npj Computational Materials 5, 41 (...
15
votes
2answers
104 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 ...
15
votes
1answer
307 views

CCSD(T) Transition State and Ground State Calculations in Gaussian09: “Unable to Determine Lambda”?

I’m doing CCSD(T) calculations (for both transition and ground state geometries) on a series of small molecules in Gaussian09. Several similar calculations terminated without any problems but one TS ...
14
votes
1answer
176 views

How the projected density of states is built

I'm new to DFT. I'm trying to figure out how projected density of states (PDOS) is built in solid state physics software package. I understand the basics of the density functional theory method: each ...
14
votes
1answer
223 views

How can I scan the whole PES of a bulk structure?

I am not very familiar with scanning a PES for a bulk structure, and I'd be very appreciative for some suggestions.
13
votes
4answers
189 views

What is the role of a chemist in computational chemistry?

As someone that wants to learn about computational chemistry, mainly for its use in energy storage materials (and therefore DFT as the most practical method of it), I am wondering what is essential ...
13
votes
2answers
267 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: ...
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, ...
13
votes
2answers
172 views

A CCSD(T) geometry optimization in Gaussian09 is deviating too far from the minimum. How do I deal with it?

I am doing a CCSD(T) geometry optimization on a series of molecules. One of the geometry optimizations took about 2 weeks even though an analogous molecule with the same number of basis functions took ...
12
votes
1answer
92 views

What is the impact of the orientation of a molecule in cartesian coordinates to molecular properties?

According to my knowledge, each computational chemistry code optimizes a molecule keeping the input orientation of the molecule. The population and spectral analysis is performed on the optimized ...
12
votes
1answer
64 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....
12
votes
1answer
120 views

Calculate spin-spin coupling based on previous GIAO calculation with Gaussian

I used GAUSSIAN/GAUSSVIEW to calculate the GIAO Magnetic shielding tensor (ppm), but I forgot to calculate the Nuclear spin-spin coupling J (Hz). How can I use the .chk file or .log file to calculate ...
11
votes
2answers
240 views

One-center two-electron integrals between 1s STO

As per @user1271772 's suggestion I am asking this question here again. I am trying to understand SCF cycle by trying to code up solved example from Quantum Chemistry by Levine (page 443, 5th edition)...
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 ...
11
votes
1answer
158 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 ...
11
votes
1answer
192 views

How to get more significant digits from OpenBabel?

I am generating conformers from SMILES string using OpenBabel. The shell script looks something like: ...
11
votes
1answer
226 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 ...
11
votes
1answer
128 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 ...
11
votes
0answers
76 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) ...
10
votes
3answers
539 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 ...
10
votes
2answers
95 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 ...
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 ...
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 ...
10
votes
1answer
109 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
118 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 ...
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 ...
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 ...
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 (...
10
votes
0answers
101 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 ...
10
votes
0answers
70 views

What are the methods of modeling Jahn-Teller effects in a solid-state material? [closed]

The Jahn-Teller effect arises from the symmetry breaking (distortion) of the local environment for the crystal field of 3d transitional metal ions.The distortion result in energy saving of electronic ...
9
votes
3answers
377 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
239 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
387 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
2answers
463 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 ...
9
votes
1answer
163 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 ...
9
votes
1answer
409 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 ...
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 ...
9
votes
1answer
43 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 ...
9
votes
0answers
86 views

Is there any literature that systematically analyzes current quantum chemistry algorithms using Big O notation for time and memory cost? [closed]

Big O notation is commonly seen in the papers on novel computational methods. However, only a few of them include rigorous analysis of the algorithm. Is there any literature that summarizes current ...
8
votes
2answers
252 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 ...
8
votes
1answer
152 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 ...
8
votes
1answer
174 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: ...
8
votes
1answer
62 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 (...
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 ...