Questions tagged [computational-chemistry]

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

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9
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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 ...
7
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0answers
491 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 ...
5
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0answers
87 views

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 \;} \\\\ \...
1
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24 views

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, ...
1
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0answers
35 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 ...
1
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0answers
76 views

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 ...
1
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0answers
54 views

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 ...
1
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0answers
256 views

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 ...
1
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0answers
88 views

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^{*}\...
1
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0answers
136 views

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 ...
0
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0answers
25 views

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 ...
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18 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 ...