Questions tagged [monte-carlo]
For questions related to Monte Carlo methods, which solve deterministic numerical problems via a probabilistic sampling approach.
24
questions
3
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0answers
15 views
Proper normalization of the radial distribution function to take into account unlike pairs only
In calculating a radial distribution function for a simulation for a few thousand molecules, I loop over unlike pairs and calculate the radial distribution function with respect to a particular site ...
6
votes
0answers
57 views
Some questions about implementing Swendsen-Wang algorithm
I have a lattice system with two types of sites, namely A and B. Both A and B have a possible up or down spin orientation. There exists $J_\textrm{aa,align}/J_\textrm{aa,mis}$, $J_\textrm{bb,align}/...
8
votes
0answers
45 views
Benchmarking Monte Carlo simulations of polymers
I have written a simulation engine in C++ to run a Monte Carlo simulation of polymers on a lattice. My code basically plants a polymer on a lattice, and performs certain Monte Carlo moves, including ...
7
votes
0answers
77 views
Normalizing the radial distribution function [closed]
The radial distribution function is defined as:
$$g(r)=\frac{dn}{4\pi r^{2} dr \rho}.\tag{1}$$
Why, in the calculation, do you divide twice by the number of molecules? What I mean is something like ...
8
votes
1answer
83 views
How often does one have to run polymer Monte Carlo moves to effectively sample phase space?
I have a polymer and solvent on a lattice, and I am performing an NVT Monte Carlo simulation. I am performing the following moves on it:
My question is, how should these moves be conducted to ...
14
votes
2answers
409 views
How do you incorporate hydrogen bonding into molecular simulations?
How do computer simulations of liquid hydrogen-bonding systems incorporate hydrogen bonding? Since I think hydrogen bonding has mixed covalent and electrostatic character, wouldn't you need something ...
4
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0answers
28 views
Discrete lattice polymer simulations
I am trying to develop phase coexistence curves for generic polymers. Of course, I can use standard Flory theory free energy functionals to do this, but I want to define my nearest neighbor polymer-...
4
votes
1answer
77 views
Simulating polymers using cellular automata?
I am a physics student, and I am working on my final year project, I am planning to simulate polymers using cellular automata. I am really struggling with this project, if someone can give me any ...
12
votes
1answer
118 views
Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance
I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm.
I first load a default system of particles (alanine-dipeptide in ...
9
votes
2answers
125 views
Starting configuration for a molecular simulation
When doing a computer simulation, what’s the best way to prepare a starting configuration to avoid biasing your results?
The book Computer Simulation of Liquids suggests putting the molecules on an ...
9
votes
1answer
473 views
Why is specific heat not zero at absolute zero?
In this old paper on Monte Carlo simulations of Lennard-Jones solid, specific heat behaviour (both $c_p$ and $c_v$) have been reported. As you can see from the picture below, both $c_p$ and $c_v$ goes ...
16
votes
2answers
595 views
Is there a more efficient hard sphere packing algorithm?
I am trying to pack hard-spheres in a unit cubical box, such that these spheres cannot overlap on each other. This is being done in Python.
I am given some packing fraction ...
12
votes
1answer
420 views
Are there examples of ab initio predictions on small molecules without the "major approximations"?
In most textbooks the precise Schrödinger euqation of a molecule is given (and the "beautiful thing" stops here), then born oppenheimer approximation is made, then layers of other ...
14
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2answers
1k views
Classical Monte Carlo vs. Molecular Dynamics
Both Classical Monte Carlo (MC) and Classical Molecular Dynamics (MD) simulations are used to perform simulations of ensembles of molecules. These MC calculations are calculating thermodynamic ...
11
votes
1answer
190 views
How does one compute the boiling point of a liquid made of a particular molecule?
This question is in relation to Anomalous boiling point of "iso-" alkanes on Chemistry SE.
I want to compute the boiling point of the different isomers of an n-carbon alkane to check what ...
9
votes
0answers
100 views
Coupling between 1st and 2nd order phase transitions? [closed]
I am seeking some models or references on how to couple, or what to take into consideration, while coupling first-order phase transitions (for magnetic systems) and second-order phase transitions, in ...
14
votes
0answers
195 views
Why does the Wolff algorithm slow down in a 4-body Ising model?
In the paper that introduced "Self-learning MC" (an ML-inspired MC technique, as I understand) the authors consider a many-body Ising model as an example to show the efficiency of their ...
13
votes
3answers
261 views
What are the types of Quantum Monte Carlo?
Similar to:
What are the types of SCF?
What are the types of MCSCF?
What are the types of ab initio Molecular Dynamics?
What are the types of pseudopotentials?
What are the types of DFT?
What are the ...
19
votes
1answer
115 views
How can very small lattices be sufficient for Quantum Monte Carlo simulations?
Quantum Monte Carlo simulations are often performed with very modest lattice sizes (such as [e-print], $64$ sites), due to their computational cost increasing exponentially with the system volume; ...
12
votes
2answers
284 views
Autocorrelation function problem in Monte Carlo simulation of 2D Ising model
Currently, I did a Monte Carlo simulation with the local update and Wolff cluster updated in 2D classical Ising model. I use the autocorrelation function to compare 2 different algorithm in critical ...
12
votes
2answers
77 views
In Monte Carlo: does nonequilibrium imply stationary state?
I'm currently responding to referees about a manuscript on the dynamics of the Ising model. I have been using the term nonequilibrium to refer to any state that is not characteristic of the ...
17
votes
2answers
128 views
How to simulate atomic scattering from solid walls at finite temperature for a particles in a box simulation?
I'm not sure if this will be considered on-topic, let's see what happens. I've asked this previously in Physics SE and it was closed as needing focus. It is now past 30 days and too late to consider ...
15
votes
1answer
94 views
What are the modelling techniques that can be used for simulating microstructure evolution in materials?
I am aware that the Potts Model can be used to simulate grain growth, and that Phase Field Models have also been very successful. What are the advantages and limitations of these models? What are the ...
15
votes
1answer
152 views
What is the definition of ergodicity in Monte Carlo?
I've been writing a manuscript about the breakdown of ergodicity in single spin flip Metropolis algorithm Monte Carlo arXiv:2001.09268.
The definition I have been using is: a Markov process is ...