The branch of chemistry dealing with the use of mathematical models to solve problems in chemistry.
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17 views
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 ...
2
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0answers
36 views
Trying to generate a wave function basis set
For a little project I'm working on, I am trying to generate a wavefunction basis set I can use in Quantum Monte Carlo (DMC to be specific). Preferably, it would be a linear combination of Slater ...
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0answers
22 views
How can I know the distance of an atom from the heli's axis in GROMACS? [closed]
I am looking at the structure of iota-carrageenan double-helix.
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0answers
53 views
Extracting geometry data from Gaussian09 geometry optimization
I want to extract the geometry for every single step of a Gaussian09 optimization from the .log file. I need the results in cartesian XYZ format, either in one file or in multiple files.
First I ...
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0answers
50 views
Calculating AIC (in R or any other statistical software)
I am trying to fit the log-log plot of the cumulative distribution of a network to one of three models: Exponential (EXP) ($P(k)\sim e^{-ak}$), Exponentially truncated power law (TRU) ($P(k)\sim ...
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7answers
629 views
Does Computational Science involve programming?
I read about computational science on Wikipedia, but my understanding is not very clear.
Does computational science involve programming? How different is computational science from computational ...
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1answer
57 views
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 ...
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4answers
354 views
Best hardware solution for microsecond Molecular Dynamics
We would like to reach Molecular Dynamics simulation of proteins with around 20000 atoms in explicit water with trajectories of around 1 microsecond each. We are looking at different options for ...
10
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4answers
413 views
good (free) software for producing publishable images?
I am producing 1d and 2d images using Matlab right now for comparison of accuracy against a given model. I need to compare my methods with the standard Gaussian .wfn model and I am going to do that by ...
2
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1answer
113 views
In molecular dynamics (MD) simulations, how is particle number density computed in practice?
I have been reading a recent paper. In it, the authors performed molecular dynamics (MD) simulations of parallel-plate supercapacitors, in which liquid resides between the parallel-plate electrodes. ...
7
votes
4answers
315 views
Making a Molecular editor/visualizer: Object oriented programming, data structures, and molecules
I am new to programming and I am trying to solve my first big problem and write my first big program. I have looked for open source examples of code to learn from, but so far have only found code in ...
5
votes
1answer
233 views
Implementing simple atom model using density functional theory (DFT)
I am trying to write computer code which will find the energy and density function for a atom with Z protons and N electrons. I am working in 1D for simplicity and would like to make the overall code ...
9
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2answers
234 views
How can one mathematically describe the “cartoon” type of representation of proteins?
Proteins are typically represented in a cartoon form, with β sheets as arrows and α helices as coils:
I'm wondering, is there somewhere a reference that describes the construction of this ...
6
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3answers
277 views
Why does iteratively solving the Hartree-Fock equations result in convergence?
In the Hartree-Fock self-consistent field method of solving the time-independent electronic Schroedinger equation, we seek to minimize the ground state energy, $E_{0}$, of a system of electrons in an ...
6
votes
4answers
494 views
Are open-source codes available to study protein folding?
I would like to test the influence of solvation parameters in implicit solvation models and wonder which codes are freely available as standalone programs for protein folding of small proteins, and ...
6
votes
2answers
98 views
Can quantum methods be applied to the protein-ligand docking problem?
In the problem of protein-ligand docking, most of the time people are happy if they can just predict the final conformation the ligand adopts into the protein's binding pocket. Most of the time one ...
3
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1answer
89 views
What is the difference between ECPs and ADF frozen cores?
As the title suggests, what are the differences between the frozen core approximation as implemented by Amsterdam Density Functional and effective core potentials (ECPs)?
2
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2answers
467 views
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 ...
11
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1answer
303 views
Enumeration of graphs deriving from Delaunay tessellations in 3D
Is there an algorithm that enumerates the graphs that correspond to some Delaunay tessellation of points in 3D?
If so, is there an efficient parameterization of geometries that correspond to any ...
6
votes
5answers
372 views
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 ...
5
votes
4answers
324 views
Where can I find a database of simple chemical structures in XYZ format?
As from Title. Where can I find a database of simple chemical structures in XYZ format, possibly with a simple CAS -> XYZ or InChi -> XYZ REST service ?
4
votes
2answers
224 views
Pauli repulsion contribution in electronic structure computations
I am looking for a method to estimate the contribution from Pauli repulsion to the interaction energy of a molecular dimer in an electronic structure computation (e.g. with Density Functional Theory). ...
8
votes
2answers
609 views
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 ...
8
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2answers
1k views
How is B3LYP implemented in Gaussin 0*, GAMESS-US, Molpro, … etc?
Specifically I want to extend work involving B3LYP started with Gaussian 03 but continued with GAMESS-US. The energies provided by the default B3LYP methods are not the same. There is a discussion ...
2
votes
3answers
251 views
Differences between Gaussian and Slater functions on the quality of the results?
Given two computational programs, one using a Gaussian basis, and the other using Slater basis, what are the practical differences, advantages and disadvantages for each choice ?
8
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2answers
166 views
What does it mean for a basis set to be “correlation consistent” ?
Some basis sets are said to be "correlation consistent". What does it mean in practice ?
7
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1answer
225 views
How to choose a basis set for ab-initio evaluations ?
How do I pick a basis set for an ab-initio Hartree-Fock evaluation ? In other words, what are the important characteristics of a basis set so that a proper choice can be made ?
6
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2answers
735 views
What is counterpoise correction?
What is counterpoise correction exactly ? Can you explain when it is needed and why ?
12
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3answers
239 views
Is Hartree-Fock always a good approximation for molecular geometries and no bond breaking ?
Are there cases where Hartree-Fock is not a good approximation to compute equilibrium geometry when the molecule is in a non bond-breaking condition?
6
votes
2answers
120 views
What is the difference between Coupled Cluster SD and SD(T)?
Can you explain the difference between these two computational methods ?
