Questions tagged [computational-chemistry]

The branch of chemistry dealing with the use of mathematical models to solve problems in chemistry.

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Are there any standardized file formats for point group character tables?

Character tables are an important tool for symmetry analysis in many computational chemistry software packages. Are there any standardized file formats for point group character tables? This may seem ...
jvtrudel's user avatar
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8 votes
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577 views

DIIS method to accelerate SCF convergence for stretched geometries

I am implementing from scratch an Hartree-Fock calculation in the STO-3G basis set to perform Born-Oppenheimer molecular dynamics. I have a Restricted Hartree-Fock procedure that can reproduce very ...
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Evolutionary dynamics in vascularised tumors, PDE-ODE coupled system

I have to solve the following PDE-ODE system $$ \displaystyle{\partial_{t} n = \bigl[a(s) - b(s)(y - h(s))^{2} - d\int_{\mathbb{R}} n \, dy \; + \; \beta \, \partial^2_{yy} n \;} \\\\ \...
AleManara's user avatar
2 votes
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Newton-Raphson with Zeroth-Order Continuation is not Converging

I am trying to solve this system of nonlinear equations using Newton-Raphson method with continuation (zeroth-order continuation). $F_1(x, y, \xi, \nu) = \left(1 - \frac{1}{\nu}\right) \left(1 - x\...
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2 votes
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Calculating the species mass consumption from implicit reaction-term in diffusion-reaction equation

The 1D diffusion equation with a chemical source term has the following form: $$\frac{\partial Y}{\partial t} = D \frac{\partial^2 Y}{\partial x^2} - k Y,$$ where $Y$ is the molar concentration of the ...
user306429's user avatar
2 votes
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Calculate activation energy of inter molecular displacement on a nano particle

I'm simulating a nano particle and wish to calculate the activation energy of the reaction where an atom is displaced from one point on the lattice to a neighboring void( might be at higher energy ...
fireball.1's user avatar
2 votes
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What are alternatives to openbabel to convert CML file to image?

I recently started to perform natural resonance theory (NRT) analysis with NBO6. This program may automatically create a chemical markup language (cml) file with the treated structures. Unfortunately ...
Martin - マーチン's user avatar
1 vote
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Why is scoring a separate problem even after docking is done?

With regards to protein-ligand interactions, we talk about two concepts, docking and scoring. I understand that docking means to find the best orientation of a ligand at the active site of a protein, ...
Mahathi Vempati's user avatar
1 vote
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117 views

Tight binding model calculation with Extended Huckel Approximation

I've been reading Albright's Orbital Interactions in Chemistry. In the chapter on solids, he provided a general approach to find the band structure of a solid state system Now if we are to model a ...
Macrophage's user avatar
1 vote
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Parallelizing molecular simulation with full configuration energy

First, let just me stress that I'm not a an expert in computation chemistry, so now the problem: We have GCMC molecular simulation, in the Grand Canonical ensemble, using the standard metropolis ...
dual0's user avatar
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Time dependent self-consistent equations

I am facing the following problem. I need to solve numerically a set of coupled equations $$i\frac{d}{dt}f_{n}^{(i)}(t) = \left[U\cdot n(n-1) + \mu\cdot n\right]f_{n}^{(i)}(t) - \sqrt{n+1}\Phi_i^{*}\...
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Center of Mass for molecule in Gaussian09

Gaussian09 prints coordinates where the local coordinate system as center at $C = (\Sigma n_i*X_i)/(\Sigma n_i)$ where $n_i$ is the Mass Numer of the atom. However, the Mass Number is not actually ...
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pp.x command in quantum espresso

I am trying to generate the .pp and .cube file using pp.x -i (input file name) command. But, the .cube file is not getting generated and the output.log file also shows an error message. this is my pp....
Bilal Ahmad's user avatar
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192 views

Optimising transition state geometries using gaussian 16

I'm attempting to carry out transition state optimisations in Gaussian and a lot of my calculations are coming up with errors, the main one being no analytic 2nd derivatives for this method. How can ...
Beth's user avatar
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Examples of kinetic modeling with optimization techniques in Python

We are looking for studies or tools that implemented kinetic modeling with parameter estimation differential evolution or similar optimization techniques in Python. We are trying to understand what ...
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Reference request: Textbook similar in structure to "Computational Materials Science: An Introduction" by June Lee for Computational Biology

In the Computational Materials Science: An Introduction by June Lee, he discusses molecular dynamics and density functional theory with examples from LAMMPS and QuantumEspresso, and explains LAMMPS ...
Josh's user avatar
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Moller Plesset Theory- MP2 correction

I have a molecule LiBH2 with C2V point group. I used 3-21G basis set and obtained RHF coefficients and symmetry of orbitals. I wish to find the set of orbitals (a,b,i,j)( where a and b are occupied ...
Tapasvi Bhatt's user avatar
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219 views

How to handle system of chemical reactions for a batch reactor SciPy solver

I have a system of chemical reactions where the rate equations represent a batch reactor model. The model is a system of ODEs which is solved with the SciPy ...
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