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Questions tagged [computational-chemistry]

A field which employs computers to model and study chemical systems and chemical behavior, using various models, from approximations of the Schrödinger equation to Monte-Carlo simulations, to modeling with differential equations.

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Suggestions for switching from computational materials science to computer-aided drug discovery

I'm wrapping up my PhD in computational materials science and my focus has mainly been inorganic semiconductor materials for device applications. I'm really intrigued by computer-aided drug discovery ...
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Convert CONTCAR to .cif file

i got a CONTCAR file and like to convert to .cif file. Could someone help me to with any source code to convert this? Thanks in Advance !!
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14 views

GAMESS Gaussian qst2 method alternative

I've heard about the qst2 Gaussian method but I don't have any licence so I use the free GAMESS-US. Nevertheless, I didn't find any Gamess method which allows a TS finding like qst2. Have you heard ...
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Gaussian syntax error on the input line

I ran a Gold complex in Gaussian 09 with the following exact Route Section PBE0/LANL2DZ Opt Freq NoSymm and it gave me this error message: ...
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22 views

Optimized General Contractions using the EMSL Basis Set Exchange

When using the EMSL BSE Database and selecting a basis set, one can choose the "Optimized General Contractions" or not. When doing so for, e.g., Nitrogen and the cc-pVDZ some basis functions are not ...
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1answer
21 views

Help with missing output from cubegen utility after density calculation in Gaussian16

I am busy trying to do density calculations in Gaussian16 as I need the .cube output for input to the PIXEL software. But my Gaussian output seems to be missing an entire chunk of data and I don't ...
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What is the largest coupled cluster calculation that has ever been done (as of March 2019)?

I am doing some research and trying to make sure the numbers I am reporting are accurate. I found that the paper by Sylvetsky et. al. says:[1] We were, however, able to complete a ...
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42 views

Is NWChem not respecting Hund's rules when performing a calculation on the oxygen atom? [closed]

I made a calculation with NWChem (Version 6.8) using the SCF method, the aim was to discover the method by doing simple calculations on a oxygen atom $\ce{O}$. Some results are surprising me, one of ...
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1answer
51 views

HCl rota-vibrational lab: ab initio simulation of rotation constants

I'm trying to set up the simulation portion of the classic undergraduate lab studying the rotavibrational spectrum of HCl and DCl. In terms of simulation (using Gaussian 16), the equilibrium ...
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1answer
235 views

Perturbation theory in Quantum/Computational Chemistry

As we know, the common methods for computation molecular properties in modern Quantum/Computational Chemistry is the Hartree–Fock method and Density Functional Theory. But from university course of ...
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2answers
101 views

Molecular orbitals used with CCSD(T) geometries

Suppose I am given some geometry data (say, of a water dimer) from CCSD(T). If I were to do a single-point energy calculation to generate orbitals for the system, wouldn't CCSD give something more ...
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71 views

relaxed dihedral PES scan: symmetry of the system not reflected

Using G16 and performing a relaxed PES scan on a dihedral angle, I performed 72 steps where one phenyl group of a symmetric terphenyl is rotated about the C(aryl)-C(phenyl) bond by 5° in every step. I'...
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2answers
101 views

Ab initio calculations

Why are quantum mechanical calculations so computationally expensive? What exactly is the process that makes it so time taking?
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Best Gaussian Basis sets which almost perfectly fits with the slater type orbitals

What is the best Gaussian basis sets to represent the slater type orbitals perfectly particularly $1s,2s,2p_{x},2p_{y},2p_{z}$ with slater exponent $\zeta=1$.Please suggest some references of those ...
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21 views

Is the 12-6 Lennard Jones potential a good description of van der Waals interaction energy?

It seems to me that the Lennard Jones potential oversimplifies the more complex nature of van der Waals forces. However, in most of the MD simulation package, this is generally accepted.
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Why the use of MD simulations is less popular for the study of carbohydrates?

In classical all-atom MD simulations, the force fields for proteins, nucleic acids and lipids seem to be more well developed than carbohydrates. It seems to me that the use of MD simulations is not so ...
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1answer
34 views

Calculate pKa for lipids

I would like to calculate $\mathrm{p}K_\mathrm{a}$ of lipid molecules using some software tools. I have tried ChemAxon and compared with ChemDraw professional 16.0 version they are mostly similar. I ...
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26 views

NMR Prediction for compounds at variable pH values

Like the title says, I'm looking for any software package that may be able to simulate a variety of NMR at a variety of different pHs. The majority of the software programs that I've found do not have ...
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0answers
27 views

What command to use to make ORCA to ignore the electron-electron repulsion term in the Hamiltonian?

I am trying to solve $H_{2}$ molecular Hamiltonian in the presence of two nuclear centers without the electron-electron repulsion term. what command to use to make ORCA print core Hamiltonian which ...
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1answer
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How do water models fit into force field methods?

What I Understand: In molecular mechanics, it is recognised that molecules tend to be composed of units that are structurally similar in a vast array of environments so atom types are defined from ...
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1answer
39 views

Mixing of molecular orbitals in polyatomic molecules

I am trying to solve the following Hamiltonian,$$H=-\frac{1}{2}\nabla^{2}-\sum_{i=1}^{10}\frac{1}{|\vec{r}-\vec{R_{i}}|}$$ Here $Z=1$ . To get all ther molecular orbitals of this system. I took the ...
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0answers
52 views

How do I calculate the full configuration interaction Hamiltonian of H2

I have been trying to follow the paper titled "Towards Quantum Chemistry on a Quantum Computer" (https://arxiv.org/pdf/0905.0887.pdf) by simulating their results on a quantum computer simulator. ...
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3answers
88 views

How to index molecules in computer programs? [closed]

Is there a standard way how can the index over a molecular structure be kept in the computer? A molecule is a graph, where nodes have labels (chemical element type), and edges are chemical bonds. ...
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0answers
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Good software/module in python to determine nuclear attraction integral in Slater type orbital basis sets

I am trying to solve a Hamiltonian of one electron and 10 stationary nuclear centers. here, the electron is treated quantum mechanically and nuclear centers are treated classically objects. The ...
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1answer
46 views

Why is the ROHF spin density of the propenyl radical not symmetric?

I was preparing some material for my students and in order to illustrate the concept of spin density and how the ROHF method gives a purer description of this property than the UHF method. I prepared ...
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0answers
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Amber Force Field Improper Parameterization Huge Kb Problem

I am trying to parameterize a molecule. I know dihedrals and impropers are the same for Amber Force Field. (Source: http://archive.ambermd.org/201004/0334.html) So, I did PET scan for improper and I ...
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0answers
60 views

Know if a molecule is viable with Python [closed]

I'm working with python and I'd like to know if someone knows a python module which is able to check if a molecule is chemically viable (valence, connectivity constraints ...), or not. I know there is ...
2
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0answers
60 views

Amber paramfit “monomer (or ligand)” problem [closed]

I am trying to parameterize a novel molecule which has atoms not included gaff or parm force field. I finished parameterizing vdw-bond and angle force field. Also I did PES Scan for dihedrals and I ...
2
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1answer
56 views

Radial pair distribution function (VMD). How to define it for a water NaCl system with multiple Na and Cl?

I'm struggling to understand a paper in which someone has presented radial distribution functions (RDFs) for a system that contains multiple Na, Cl, and water atoms/molecules. I don't know exactly ...
5
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0answers
57 views

Ab initio MD simulations in VASP

I'm not sure if this is an appropriate question for Chemistry.SE, but I'm taking a stab. I'm running ab initio MD calculations in VASP and I'm trying to optimize different input tags. On the VASP ...
8
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1answer
92 views

How do the def2-SV, def2-SV(P), and def2-SVP basis sets differ?

I am trying to calculate the energy of complex molecules with DFT and have a question about the Ahlrichs (Karlsruhe) def2 basis sets. What is the difference between the def2-SV, def2-SV(P), and def2-...
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1answer
41 views

Molecular Orbital Mixing to get the Molecular Orbitals of a large molecule

I am trying to get the molecular orbital for arbitrarily placed nuclear centres (identical). In other words , I am trying to solve the following one electron hamiltonian. $$h=-\dfrac{1}{2}\nabla^{2}-\...
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0answers
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tolerable error, CASSCF simulation of UV/Vis spectrum

Please forgive my ignorance of experimental spectroscopy. I am a computational chemist, not an experimental one. My question is: what would be considered a tolerable or reasonable difference between ...
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1answer
83 views

Conformer generation for radicals

Is there an automatic way to generate conformers for radical like systems (spin multiplicity is doublet)? My system for the study is a substituted fullerene with a missing H atom from the functional ...
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0answers
32 views

Natural orbital population analysis in Gaussian

Within (restricted) density functional theory and Hartree-Fock, respectively the Kohn-Sham orbitals and spin orbitals are the natural orbitals, with occupation numbers either 2 or 0. As I understood, ...
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1answer
81 views

How to Calculate Lennard-Jones Parameters from TDDFT?

I am trying to develop parameters for AMBER force fields and to calculate Lennard-Jones parameters for the $\ce{Fe^3+}$ ion. I did a deep search and found that the best way to do this with a high ...
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1answer
102 views

Overlap matrix (H2 molecule, STO-3G) [closed]

I'd want to implement SCF method using Modern Quantum Chemistry (Szabo). But when I want to calculate overlap matrix for H2 (STO-3G basis) my results aren't equal to true overlap matrix that there's ...
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0answers
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What algorithm is GaussView using for the clean function?

A colleague showed me GAUSSIAN 09 which comes with GaussView 5 for drawing structures. What impressed me was the snappiness of the Clean function. What algorithm is used for the Clean function? The ...
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2answers
93 views

How To Scan “improper dihedrals” in Gaussian 09?

I am trying to parameterize Amber force field for a novel molecule, but I couldn't obtain improper dihedrals. Because if I scan impropers like dihedrals; later or sooner the molecule is overlapping ...
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0answers
35 views

Generating density matrix of a wavefunction from common quantum chemistry software

I am looking for density matrixes for a couple of closed shell and open-shell systems, and I wonder if there is a trivial way to make e.g. Gaussian just generate an output for me. I may be wrong but ...
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1answer
55 views

Why do people add H(core)+F in Hartree-Fock?

I'm trying to implement my own HF code, and it seem usual that, after building the Fock matrix $F$, they add that to the pre-existing $H_{core}$, from the two-point interactions, when computing final ...
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0answers
120 views

Inverse problems in Computational Chemistry: The case of Inverse eigenvalue Problems for molecule structures

Mathematics Background An inverse eigenvalue problem (IEP) is the problem of reconstructing a matrix with a special structure from prescribed spectral data. By structure we mean the pattern of ...
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Geometry optimisation in Gaussian09

I have looked at various sources regarding this, including the Gaussian official website. However, I have not managed to understand the geometry optimisation method used by Gaussian, a method known as ...
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0answers
14 views

Computational method to model the interactions between a liquid, a solid surface and particles on it?

I’m looking for a way to model the interactions between a liquid, a surface and various particles over the surface, in order to simulate the cleaning of said surface with different substances. My ...
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0answers
39 views

Putting high symmetry points labels to a band structure plot

So far I've got this plot using Quantum Espresso. I want to put gamma, X, L, etc labels to the k-path. Quantum Espresso's ouput states the following: ...
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0answers
13 views

Lipophilicity computational prediction

Is there a web based (or otherwise) computational chemistry tool which is able to calculate lipophilicity of a given compound?
5
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1answer
88 views

Raman spectra in Gaussian [closed]

I want to simulate Raman spectra of benzene in Gaussian 09. Calculated spectra for a single ring Benzene ($\ce{C6H6}$) in Gaussian differs about $\pu{40 cm^{-1}}$ for each peak, compared with ...
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1answer
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Does the hydrohelium dication exist?

It is well-known that there exists the $\ce{He2^2+}$ dication, and also $\ce{HHe+}$ and $\ce{H2+}$ cations. But I could not find any definite information about the existence or inexistence of the $\ce{...
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1answer
56 views

Diffuse functions for Ahlrichs/Karlsruhe basis sets in Gaussian?

As the question states, can one use the basis sets of Ahlrichs and coworkers (e.g. def2-SVP, def2-TZVP, ...) with diffuse functions (e.g. def2-TZVPD) in Gaussian? The regular basis sets have been ...
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0answers
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How to understand MO diagrams for cationic octahedral transition metal complexes

I am having problems understanding the construction of MO diagrams in octahedral transition metal complexes within ligand field theory (LFT) when the metal center is asumed as an cation: I am ...