36
votes
Accepted
Approximate equivalence table between Pople's basis sets and Jensen's DFT optimized polarization consistent basis sets (pcseg-n)
Disclaimer and warning: long and likely biased answer.
Background: The Pople style basis sets were defined almost 50 years ago. The 6-31G was designed for HF calculations, the 6-311G for MP2 ...
- 1,311
25
votes
Accepted
What are the "smart algorithms" applied to solve the "curse of dimensionality"?
This is a very broad question, so I am going to give a very brief overview of typical exponentially-scaling problems. I am not an expert in most of these areas, so any suggestions or improvements will ...
- 1,918
22
votes
Accepted
Why do people care about reversibility in molecular dynamics simulations?
This is an excellent question! Reversibility in MD is useful because:
Time-reversibility in a numerical integrator leads to a doubling of the accuracy order (see Propositions 5.2 and Theorem 6.2 ...
- 1,073
22
votes
What does B3LYP do well? What does it do badly?
B3LYP is still a decent functional at its level of theory (single-hybrid functional), but you're right that there's a general criticism of it, which I largely hear in the form of people saying things ...
- 33.6k
20
votes
Accepted
What does B3LYP do well? What does it do badly?
I think this review¹ by Head-Gordon is a useful supplement to Nike's answer. Its combines a review of functional development, a benchmarking of various functionals, and an explanation of the design ...
- 15.2k
19
votes
Accepted
What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?
Disclaimer: I'm the lead developer of Open Babel and Avogadro - and currently mentoring Google Summer of Code projects.
The biggest question is more "what kind of topics" interest you and/or what ...
- 9,045
17
votes
Accepted
Why is uncertainty not a big problem in computational chemistry?
Following your arguments, we would see also a 'violation' of the Heisenberg uncertainty principle (HUP) in single-particle quantum mechanics, e.g. in a Hamiltonian of a particle in an external ...
- 659
17
votes
GUIs for Quantum Chemistry... Where are they?
My answer to "GUI for DFT calculations" is a good introduction to my stance on this issue, but I will address your more specific questions here. First for some preliminaries:
Software ...
- 33.6k
16
votes
What does B3LYP do well? What does it do badly?
I don't have too much to add to the answers of Nike Dattani and Tyberius, but I think the crux is that its capabilities have been historically overestimated.
One particular failing of B3LYP is that it ...
- 656
15
votes
How the projected density of states is built
Disclaimer: This answer would have been better placed in a comment but since I have just joined the community I cannot write comments. Ironically, I was tipped about this community after answering a ...
- 251
15
votes
Accepted
GUIs for Quantum Chemistry... Where are they?
Gaussian has Gaussview, QChem has IQMol, Schrodinger has Maestro, Quantum ATK and BIOVIA Material Studio each have their own GUI. Notice, that both the program and GUI in these cases are paid products ...
- 15.2k
14
votes
What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?
OpenBabel
And the related Pybel are excellent platforms for starting a project because they have well written C++ and python APIs, and are specifically designed for cheminformatics 101. For example, ...
- 7,957
14
votes
How to start a Machine Learning project for chemical properties prediction?
Admittedly, there are tons of materials on the chemistry + machine learning topics. Let me give one:
An introductory text I find useful is Machine Learning in Chemistry from Janet and Kulik in ACS in ...
- 1,807
14
votes
Accepted
Can DFT simulate chemical reactions?
DFT can be used for many things. One of them is to calculate an approximation of the ground state energy of a molecule. By calculating the ground state energies of all reactants, and all products, you ...
- 33.6k
13
votes
Accepted
What are the applications of chemical graph theory?
This is a question that is answered by a straightforward literature search, here's e.g. two review papers from the 1980s:
J. Chem. Inf. Comput. Sci. 25, 334 (1985)
J. Chem. Educ. 65, 574 (1988)
as ...
- 18k
13
votes
Accepted
One-center two-electron integrals between 1s STO
Your Octave code is trying to do the integral by quadrature, which makes very little sense since it will have a huge problems with the cusp.
Since this is a one-center problem, the best approach is ...
- 18k
13
votes
Why do people care about reversibility in molecular dynamics simulations?
I would argue the main reason this is important is philosophical, linked to the history of science and determinism (as proposed by Laplace). Newtonian mechanics is mathematically reversable while any ...
- 270
13
votes
Accepted
How to get potential energy surface from GAMESS?
I know it is easy to get the PES tabulated very neatly in MOLPRO with a command like:
{table,r,scf,ccsd,ccsd_t
head, R,HF-SCF,CCSD,CCSD(T)
sort,1,2,3}
which for ...
- 33.6k
13
votes
Do bonds between the atoms influence ab-initio energies?
The bonds you draw or see in Gaussview should have no effect on the calculation (besides some minor effects in choosing internal coordinates for a geometry optimization). As you note, a bond is a ...
- 15.2k
13
votes
Improving my programming for computational chemistry/physics
My Story
As an undergrad doing my first computational research project, I was told that I would be programming in FORTRAN. I remember being very nervous about this because I had never touched FORTRAN ...
- 33.6k
12
votes
How well can we model chemical synthesis?
Okay first some basics:
For most reactions we do not need to run molecular dynamics
Molecules are like springs and obey the principles of minimum energy. Therefore, normally the dynamics of a molecule ...
- 7,957
12
votes
Accepted
How can I scan the whole PES of a bulk structure?
The potential energy surface (PES) is a 3N-dimensional function for a bulk system containing N atoms (in reality 3N-3 to account for the trivial translational degrees of freedom). For a bulk structure,...
- 10.9k
12
votes
What are the "smart algorithms" applied to solve the "curse of dimensionality"?
The curse of dimensionality is indeed a huge problem in quantum chemistry, since the possible ways N electrons can occupy K orbitals is a binning problem whose computational cost grows factorially (...
- 18k
12
votes
Accepted
High precision helium energy
The 2006 variational calculation by Schwartz is lower (more accurate) than Nakashima & Nakatsuji's 2007 energy:
...
- 33.6k
12
votes
Accepted
Which basis set should be used for a system that contains both anions and cations?
The safe choice is to use diffuse functions on all atoms. It is quite rare to run into pathological overcompleteness with standard augmented basis sets, unless you're looking at very high-energy ...
- 18k
12
votes
Accepted
How do I figure out how many monomer configurations I need for my simulation?
tldr; it depends on flexibility / number of rotatable bonds
A while ago, I answered a related question - in general, molecules with fewer "rotatable bonds" need fewer conformers geometries ...
- 9,045
12
votes
Why is uncertainty not a big problem in computational chemistry?
Indeed, due to the uncertainty relation, the electrons in a molecule do not have a definite potential energy, nor do they have a definite kinetic energy (yet they have well-defined expectation values ...
- 9,076
12
votes
Can DFT simulate chemical reactions?
In this answer I would like to supplement the existing, concise answers with some detailed contexts.
I assume that you are interested in either the thermodynamics or kinetics, or both, of a molecular ...
- 9,076
11
votes
What are the applications of chemical graph theory?
I'd just briefly add that among other things, chemical graph theory is extensively used for computing so-called "molecular descriptors", which are used to capture some "common ...
11
votes
CCSD(T) Transition State and Ground State Calculations in Gaussian09: "Unable to Determine Lambda"?
It's not a descriptive error message, but this occurs when you reach the max number of iterations for the Eigenvector Following (EF) algorithm and still haven't converged a lambda. While Gaussian uses ...
- 15.2k
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