Computational Science Stack Exchange
Computational Science Stack Exchange

Questions tagged [computational-chemistry]

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

89 questions
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How does one determine the point group of a molecule?

You've managed to finally find out how the atoms are spatially arranged on your newly-discovered molecular entity. Through, say, spectroscopic means, you are now in possession of a bunch of atom coordinates, atom types, bond lengths, bond types, and…
J. M.
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6 answers

What open source tools are available to visualize molecular vibrations?

I would like to visualize a molecular vibration that is not a normal mode. I'd like to present a static, vectorial representation of the motion, and I would like some flexibility in the vector style (size, color etc). I'm also interested in…
Yann
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What is the difference between Coupled Cluster SD and SD(T)?

Can you explain the difference between these two computational methods ?
Stefano Borini
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How does Gaussian 09 handle 'Frozen Core Approximations' and how does it compare to CFour handling?

Background I'm currently working with two quantum software packages: Gaussian 09 and CFour. CFour does a very good job giving explicit control over how you want to invoke frozen core approximations and explains how the default handling is done via…
LordStryker
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Quantum chemistry - are there potential issues to be concered about when using mixed basis sets in a calculation?

I'm attempting to model energies of a transition metal complex using hybrid DFT but having issues with the description of my metal centers. The problem is alleviated by adding extra polarization functions only to the metal centers. Is this in…
Knifex
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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 than initial). Calculating this activation energy…
fireball.1
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How to manipulate dihedral angles in pre-optimized molecule coordinates?

I want to explore the low energy states of an amino acid or a peptide by generating input geometries, defined by multiple dihedral angles of the backbone or the side chain. From these starting conformations I want to do geometry optimization to…
tmartin
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Algorithm for constructing a supercell using an arbitrary integer matrix

Software like Diamond and VESTA allow users to build a supercell by extending the structure along the basis vectors of the latttice. However, I'd like to do something more general and build a supercell from an arbitrary integer matrix…
brainandforce
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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 one dimensional hydrogen chain, let…
Macrophage
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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 the mass of the nucleus. If we instead choose $m_i$,…
drjrm3
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Thermoplastic Equation solving

I was given a problem by my professor as follows Solve the System $pV=S$ $pcT=kT+BS\frac{dG}{dt}$ $\frac{dS}{dt}=\mu(V-\frac{dG}{dt})$ $\frac{dG}{dt}=f(S,T)$ Where $p$, $c$, $B$, $\mu$ are constant and $f(S,T)$ is a function to be reasonably…
Jake
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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.x input…
Bilal Ahmad
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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 and i and j are virtual oritals) that contribute to…
Tapasvi Bhatt
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