Questions tagged [computational-chemistry]

For questions about computational chemistry.

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11
votes
1answer
110 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
49 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
37 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
171 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
1answer
48 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
248 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 ...
11
votes
1answer
129 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
3answers
364 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 ...
8
votes
2answers
124 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
78 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
0answers
45 views

How to create a Potential Energy Surface in Chemcraft?

The Chemcraft website says that it is possible to create a potential energy surface. Nevertheless, it doesn't work for my Gaussian scan job. ...
8
votes
1answer
43 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 ...
12
votes
1answer
218 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
93 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, ...
11
votes
1answer
101 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 ...
9
votes
1answer
88 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 ...
12
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0answers
66 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) ...
16
votes
2answers
60 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 ...
11
votes
2answers
126 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
235 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 ...
10
votes
1answer
169 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
118 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 ...
10
votes
2answers
224 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 ...
11
votes
0answers
91 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
1answer
370 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....
10
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 ...
11
votes
2answers
73 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
105 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 ...
11
votes
1answer
89 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 (...
18
votes
2answers
722 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 (...
9
votes
0answers
64 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
206 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
342 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 ...
8
votes
1answer
131 views

Semi-canonicalisation vs canonicalisation of the Fock matrix and orbitals

I have seen the terms semi-canonicalized and canonicalized used in relation to the Fock matrix, density matrices, and orbitals; however, I am unsure what these terms actually describe. For instance: ...
11
votes
0answers
64 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 ...
6
votes
1answer
97 views

I get an error 'Conversion from Z-matrix to cartesian coordinates failed' in Gaussian09. Any suggestions?

I'm doing my calculations using G09W. My OS is Windows 7 (64-bit). This error occurs in the frequency calculation. What's even weirder is that it seems to happen right after everything is already ...
7
votes
1answer
99 views

I get this error in Gaussian09 even though I have enough memory. “Error termination in NtrErr: NtrErr called from FIOCnC.” Any suggestions?

Whenever read-write files get to about 20Gb, I get this error. I know that, in G09, one rw file is limited to 16Gb. So I have set the software to write several RWFs. But it still keeps producing this ...
16
votes
3answers
424 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 (...
13
votes
4answers
169 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
1answer
96 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 ...
14
votes
1answer
217 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
2answers
139 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 ...
17
votes
6answers
282 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....
9
votes
1answer
102 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 ...
12
votes
2answers
229 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)...
15
votes
1answer
135 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 ...
13
votes
1answer
85 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 ...
10
votes
0answers
80 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 ...
25
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 ...
16
votes
1answer
257 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 ...