Questions tagged [computational-chemistry]

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

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Good examples of "two is easy, three is hard" in computational sciences

I recently encountered a formulation of the meta-phenomenon: "two is easy, three is hard" (phrased this way by Federico Poloni), which can be described, as follows: When a certain problem is ...
Anton Menshov's user avatar
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20 votes
6 answers
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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 ...
J. M.'s user avatar
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16 votes
7 answers
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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 ...
Sheryl's user avatar
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16 votes
2 answers
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What is counterpoise correction?

What is counterpoise correction exactly ? Can you explain when it is needed and why ?
Stefano Borini's user avatar
15 votes
3 answers
6k 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 ...
Yann's user avatar
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14 votes
3 answers
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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?
Stefano Borini's user avatar
13 votes
2 answers
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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 ...
F'x's user avatar
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12 votes
4 answers
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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 ...
drjrm3's user avatar
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12 votes
6 answers
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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 (...
Yann's user avatar
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12 votes
4 answers
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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 ...
Nate's user avatar
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12 votes
1 answer
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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 "...
Deathbreath's user avatar
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12 votes
0 answers
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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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11 votes
3 answers
1k 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 ...
James Womack's user avatar
10 votes
2 answers
2k 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 ?
Stefano Borini's user avatar
9 votes
2 answers
2k 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 ?
Stefano Borini's user avatar
9 votes
1 answer
10k views

Matlab solution for implicit finite difference heat equation with kinetic reactions

I am trying to model heat conduction within a wood cylinder using implicit finite difference methods. The general heat equation that I'm using for cylindrical and spherical shapes is: Where p is the ...
wigging's user avatar
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8 votes
4 answers
3k 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 ...
Open the way's user avatar
8 votes
0 answers
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 ...
user avatar
7 votes
4 answers
3k 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 ...
Open the way's user avatar
7 votes
5 answers
7k 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 ?
Stefano Borini's user avatar
7 votes
2 answers
401 views

What is the difference between Coupled Cluster SD and SD(T)?

Can you explain the difference between these two computational methods ?
Stefano Borini's user avatar
7 votes
2 answers
154 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 ...
Open the way's user avatar
6 votes
4 answers
1k views

How important is learning hardware/architecture for scientific computing?

Apologies if this is a bit of a soft, unclear, or opinion-based question. I'm a relatively new PhD student in a (computational) quantum chemistry group. My group develops and maintains a few software ...
tmph's user avatar
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6 votes
3 answers
6k 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 ?
Stefano Borini's user avatar
6 votes
2 answers
2k views

Borrow computational power from machines around me

I'm a computational chemist working with little computational power and dealing with increasingly demanding chemical systems. My work machines are part of a big network (mixed with windows and linux) ...
HCSthe2nd's user avatar
  • 163
6 votes
1 answer
520 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 ...
joshlk's user avatar
  • 273
5 votes
3 answers
721 views

Maximize a function of an orthogonal matrix

I'm trying to write up a small code that, given a set of normal vibrational modes for a molecule, will convert them to localized vibrational modes. To do this I'm following the procedure from J. Chem. ...
Tyberius's user avatar
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5 votes
1 answer
1k views

What determines the usual chemistry textbook plots of atom orbitals?

In elementary chemistry textbooks you often have pictures like the following one: Are there any conventions how to get them? I am not sure, but I guess that it are contour plots with only one iso-...
student's user avatar
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5 votes
1 answer
5k views

Solve rate equations with different reaction orders using SciPy ode

The image below illustrates the kinetic scheme I am trying to model. My first example focuses on the conversion of the wood-oil to non-volatiles and volatiles. The rate equations are as follows: $$ ...
wigging's user avatar
  • 325
5 votes
2 answers
394 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). ...
Toon Verstraelen's user avatar
5 votes
0 answers
101 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 \;} \\\\ \...
AleManara's user avatar
4 votes
2 answers
404 views

Choice between DAE or ODE formulation for chemical systems

Consider a simple ODE system describing the evolution of two chemical species undergoing the reaction $A = B$ : $$ \frac{dn_A}{dt} = - k * n_A $$ $$ \frac{dn_B}{dt} = k * n_A $$ We can discretize ...
Anon_Chem's user avatar
4 votes
1 answer
303 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)?
Richard Terrett's user avatar
4 votes
1 answer
1k 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. ...
Andrew's user avatar
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4 votes
1 answer
435 views

OpenFOAM precipitation/crystallisation reaction solver

This question is probably related to chemical engineers that are around this forum. I am looking into writing a solver for a precipitation reaction (struvite to be precise): A+B+C+D <=> E+F A, B, ...
user3800363's user avatar
3 votes
1 answer
2k views

Computer Build for Scientific Computing

I am currently a .NET software developer(SQL Server, ASP.NET, C#, MVC & Web Forms). In my spare time I'm researching different areas of environmental science. E.g.(Hydrology, Ecology, Atmospheric ...
IEnjoyEatingVegetables's user avatar
3 votes
2 answers
3k views

Does energy decrease with basis set size in density functional theory?

Based on the variational principle, one might expect that the ground state energy of a density functional theory (DFT) calculation will decrease as the basis set size increases. (As I understand it, ...
Max Radin's user avatar
  • 365
3 votes
1 answer
81 views

Is there any numerical application whose performance heavily depends on the division operation?

I am an undergraduate student majoring in computer science. Recently, I am interested in the division operation, which is not directly supported by some architectures. While some architectures ...
konjac's user avatar
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3 votes
1 answer
1k views

Implicit heat diffusion with kinetic reactions

I am using the implicit finite difference method to discretize the 1-D transient heat diffusion equation for solid spherical and cylindrical shapes: $$ \frac{1}{\alpha}\frac{\partial T}{\partial t} = ...
wigging's user avatar
  • 325
3 votes
2 answers
144 views

C++ library to mutate pdb residues

Are there any open source libraries available to mutate PDB protein residues? If so are do you have any examples of them?
user1876508's user avatar
3 votes
2 answers
3k 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 ...
LordStryker's user avatar
3 votes
1 answer
203 views

Non-linear flux interface condition - variational formulation

Context: I am working on implementing this paper and I am struggling to come up with a variational formulation for the Butler-Volmer interface conditions. To simplify my question I consider the ...
Bernd Schwarzenbacher's user avatar
3 votes
1 answer
325 views

Suggest methods and basis sets for a variety of systems [closed]

Please help me with any/all of the cases below. In the following cases, the named method and basis set are not suitable for the chemical systems. Why aren't they? Could you suggest a suitable method/...
ARaf's user avatar
  • 133
3 votes
1 answer
1k views

Molecular dynamics: how to calculate interfacial tension [closed]

How can one determine the interfacial tension at a solid-liquid interface using molecular dynamics? What are some good articles on this topic?
Max Radin's user avatar
  • 365
2 votes
2 answers
165 views

Starting configuration for Molecular Dynamics

I have to build a bilayer using a structure obtained in a previous MD simulation. In the structure, some chains of the molecules cross the simulation box as shown below. I added water layers to the ...
Ema 's user avatar
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2 votes
2 answers
692 views

What equation should I fit this set of data points to?

I have done an experiment Estimation of silver nitrate by potentiometric titration with standard KCl solution. A plot of $\dfrac{\Delta E}{\Delta V}$ versus Volume of KCl solution gives the ...
ntk47's user avatar
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2 votes
1 answer
338 views

Global optimization methods in computational chemistry

I'm looking for a current and comprehensive overview (like a review article) of global optimization methods and their application in computational chemistry. Mostly I'm interested in geometry ...
tmartin's user avatar
  • 209
2 votes
1 answer
107 views

Quasi-Newton Method with a Transformed Hessian

I've recently came across an implementation of the BFGS algorithm but it has an additional step where the Hessian is transformed after the each update. This transformation is done so that certain ...
Unskilled's user avatar
  • 123
2 votes
1 answer
249 views

Applications of Julia in Chemistry and Molecular Physics?

I was wondering if there are any Theoretical & Computational Chemistry (MM, QM) codes or publications out there that are based primarily on the Julia programming language?
epalos's user avatar
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2 votes
1 answer
140 views

Need help with the python code: Calculating Madelung constant CsCl crystal structure

Need help with the code to estimate the Madelung constant for CsCl lattice: Cs at (0,0,0) Cl at (0.5, 0.5, 0.5) Answer: Converged value I am getting is 0.465. ...
chola's user avatar
  • 21