Questions tagged [monte-carlo]
For questions related to Monte Carlo methods, which solve deterministic numerical problems via a probabilistic sampling approach.
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How to rigorously prove the existence of a coil-globule transition of polymers in an on-lattice simulation?
I am running on-lattice simulations of polymers. I am testing out different Hamiltonians and testing different regimes to test if they yield interesting behavior. My question is, how do I rigorously ...
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What are the similarities between MD and MC in the case of protein simulation?
As far as I understand, both MD and MC simulation methods use Force Fields.
Are there any other similarities between them?
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Regarding use of GCMC to add water molecules
I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
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Open issues in MC protein simulation?
What are some open issues in Monte Carlo protein simulation research?
I am especially interested in coarse-graining.
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1
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Why do we even need periodic boundary conditions?
According to Wikipedia -
Periodic boundary conditions (PBCs) are a set of boundary conditions that are often chosen for approximating a large (infinite) system by using a small part called a unit ...
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Molecular MC simulation is not equilibrating
Suppose, a polymer has N monomers in its chain. I want to simulate its movement using the bead-spring model.
So, I wrote the following program in Python.
Polymer chain simulation with Monte Carlo ...
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3
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1
answer
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What formula should I use to calculate the total energy of a linear polymer chain?
I am using the Bead-spring model to model a polymer chain.
Suppose, the polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
And,
I can use the following formula to calculate the total Lennard-Jones ...
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4
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Where should I apply the harmonic spring function in the case of polymer simulation?
I need to simulate the off-lattice movement of a polymer chain in a 3D space using Monte Carlo simulation. Note this is not a simulation of polymer growth; rather this is about polymer movement/motion....
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How should I calculate total potential in a polymer chain?
Suppose, a polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
When calculating total LJ potential, do I need to calculate like this:
$$E(r_{12})+E(r_{23})+E(r_{31})$$
Or, do I calculate: $$E(r_{12}...
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What does it mean by pruning and enrichment in the case of Rosenbluth method?
As far as I understand:
Pruning means deleting something.
Enrich means to enhance/increase weight.
Now my question is, in the case of pruned-enriched Rosenbluth method (PERM):
For pruning/enriching, ...
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Polymer simulation
I am absolutely new to Polymer simulation. I am trying to understand the simulation by analyzing source code written by others.
Can anyone tell me what are the differences between the following three ...
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How to construct spinodal and binodal curves from a molecular simulation?
Pretty much what the title states: what is a procedure to construct a binodal and spinodal curve (temperature against composition)?
I am running an on-lattice polymer solution Monte Carlo simulation ...
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Equilibrium vs. nonequilibrium dynamics with Metropolis Monte Carlo
How is the notion of dynamics incorporated in Metropolis Monte Carlo where time isn't built in, and can such simulations be used to distinguish equilibrium dynamics / fluctuations from nonequilibrium?
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End-to-end correlation of polymers not decorrelating
I am running Monte Carlo simulations of polymers with nearest neighbor interactions only. For benchmarking purposes, I decided to run some excluded volume simulations (no overlaps) allowed on a 3D ...
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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}/...
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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 ...
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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 ...
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8
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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 ...
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14
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2
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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 ...
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4
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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-...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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12
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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 ...
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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 ...
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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 ...
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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 ...
15
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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 ...
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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 ...
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answer
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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; ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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