24
votes
Accepted
Do we know for sure that all atomic and molecular wavefunctions decay exponentially as r goes to infinity?
I'll answer this question from the theoretical side. The exponential behavior follows simply from the Schrödinger equation. Consider the one-electron Schrödinger equation:
$$
(-\frac{1}{2}\nabla^2 + V(...
- 8,166
8
votes
Accepted
Where can I find this formula?
The formulas that the code is using can be directly read off from the code. The code simulates a two-dimensional periodic box, and calculates the distance of each atom to each other atom, namely d. If ...
- 8,166
6
votes
Effect of System Configuration on MD simulation results
If you are running a particular algorithm, then different codes should in principle give the same results. However, often algorithms require random numbers that are generated with seeds within the ...
- 321
6
votes
Accepted
How might inclusion of a Grimme dispersion correction influence a simulation of a dense liquid that is not water?
Following Tyberius's suggestion, I now turn my comment into an answer.
As always, the most reliable way of estimating the effect of the dispersion correction is to actually do two simulations, one ...
- 8,166
5
votes
Are there any codes to study magnetic materials?
Another option is ALF (Algorithms for Lattice Fermions), an auxiliary-field quantum Monte Carlo package. According to its website:
it can simulate any Hamiltonian that can be written in terms of sums ...
- 786
5
votes
Are there any codes to study magnetic materials?
In addition to those listed, Spin-W is another option:
SpinW is a MATLAB library that can plot and numerically simulate magnetic structures and excitations of given spin Hamiltonian using classical ...
- 1,481
5
votes
Are there any codes to study magnetic materials?
If you already know the electron spatial wavefunctions, then it should be possible to calculate the spin exchange coefficients between electrons on neighboring atoms (by directly integrating them) and ...
- 6,469
4
votes
In which theoretical framework does the size of an atom depend on the temperature of the gas (Bose-Einstein condensates)
In calculations of the electronic energy/wavefunction, temperature typically is not taken in to account (besides cases of orbital occupation smearing, though this is used more as a computational trick ...
- 14.5k
4
votes
Accepted
What is the relationship between periodic boundary and the simulation box?
Some pseudo-code
...
- 4,266
4
votes
Accepted
Why do we even need periodic boundary conditions?
In (Metropolis) Monte Carlo one should be generating random changes in coordinates such that
\begin{equation}
X_{new} = X_{old} + \Delta X
\end{equation}
and we used a random number to generate $\...
- 4,266
4
votes
What formula should I use to calculate the total energy of a linear polymer chain?
The difference between total potential energy and total energy is just the kinetic energy, which is the sum of the kinetic energies of your particles, $$E_K = \frac{1}{2}\sum_{i=1}^3 m_i v_i^2$$
where ...
- 760
4
votes
Accepted
What are the more efficient, or easier, methods of handling electromagnetic interactions?
You could simplify long range interaction by reducing precision with range. Useful algorithm for it is:
https://en.wikipedia.org/wiki/Barnes%E2%80%93Hut_simulation
It is usually used for gravity, but ...
4
votes
elastic constants transformation/basis change P21/a -> P21/n
In order to define the matrix transforming the P21/n structure into P21/a it is imperative to know the unique axis of both space groups.
For example the contracted P21/n symbol can be used for the ...
- 641
3
votes
How to calculate the exchange matrix of a bilayer magentic system?
But in order to do that I need the exchange matrix of Co-CoO system
which should include the constant which represents the interaction
between spins in the Co part, spins in the CoO part and a ...
- 4,298
3
votes
Accepted
How should I calculate total potential in a polymer chain?
You'll want to add up all interactions that you can, up to some appropriately chosen cutoff distance. Choose the VDW cutoff such that the total energy doesn't change much if you further increase this ...
- 760
3
votes
Accepted
Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins
You simply cannot go past Allen and Tildesley's Computer Simulation of Liquids as a standard textbook on molecular dynamics. Here is a particularly illuminating diagram:
As the diagram says: (italics ...
- 1,016
1
vote
What does it mean by a "site" in the case of a CG model?
As the comments have already noted, a site in an atomistic model is the location in space at which interactions occur. The most obvious thing to do is to place all interaction sites at the atomic ...
- 3,249
1
vote
What do we simulate with molecular simulation of proteins in the theoretical research?
As @Tyberius mentioned, you can study many different things using Molecular Dynamics simulations of proteins. My senior had studied the structure and dynamics of Intrinsically Disordered Proteins (...
- 705
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