# Tag Info

### How do you incorporate hydrogen bonding into molecular simulations?

The short answer is that, while hydrogen bonds do have some covalent character, you can mimic that covalent character by increasing the electrostatic term. For example you can specify point charges to ...
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### Classical Monte Carlo vs. Molecular Dynamics

One important difference between Monte Carlo (MC) and Molecular Dynamics (MD) sampling is that to generate the correct distribution, samples in MC need not follow a physically allowed process, all ...
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### How does one compute the boiling point of a liquid made of a particular molecule?

I would like to start off by saying this is first and foremost a thermodynamic problem. Secondly, and as a result of thermodynamics, refer to Gibbs Phase Rule which says F = C - P + 2 ...
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### In Monte Carlo: does nonequilibrium imply stationary state?

This is actually a tricky question. First your use of "non equilibrium" is incorrect. Without more information on your MC simulations, especially on the applied biases and simulation process, one ...
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### What are the modelling techniques that can be used for simulating microstructure evolution in materials?

I could list the models that could be used for microstructural modeling as: Phase-Field: It is constructed based on non-equilibrium thermodynamics and Onsager reciprocal relations to derive a ...
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### What is the definition of ergodicity in Monte Carlo?

Your definition is alright, and a citable reference is Landau and Binder's A Guide to Monte Carlo Simulations in Statistical Physics which says (Sec. 2.1.3): The principle of ergodicity states that ...
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### Autocorrelation function problem in Monte Carlo simulation of 2D Ising model

@stafusa's answer is great, but there is a specific phenomenon you are encountering here called critical slowing down, which is especially bad for the single-spin-flip Metropolis Algorithm. Near the ...
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### Classical Monte Carlo vs. Molecular Dynamics

The main advantage that MD has is that alot more people have worked on algorithm efficiency. The state of the art codes for MD are really state of the art. Monte Carlo algorithms are fairly primitive ...
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### Python script for Metropolis Monte Carlo (global optimisation)

My original answer is below, but I don't think it solves your problem, because your problem is a bit deeper... if a move isn't accepted, you need to keep your old configuration, and make a new move ...
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### What are the types of Quantum Monte Carlo?

Stochastic Series Expansion (SSE) Monte Carlo Theory: SSE is a finite-temperature, discrete-time technique that works well for quantum spin problems (e.g. Heisenberg model) and other lattice ...
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### How to simulate atomic scattering from solid walls at finite temperature for a particles in a box simulation?

Whatever scattering mechanism you choose must respect detailed balance in equilibrium: on average, the number of particles hitting a patch of the wall at a given angle and velocity must equal the ...
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### How often does one have to run polymer Monte Carlo moves to effectively sample phase space?

This is a very good and tricky question, which I don't think has a clear and definite answer. I think I should also preface by saying that I can't answer it from the point of view of polymer physics, ...
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### Benchmarking Monte Carlo simulations of polymers

Alot of the early pioneering in Monte Carlo (MC) moves were done initially using lattices. While I am not directly aware of places to look for benchmarks, the pioneers in the 90's for Monte Carlo ...
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### Is there a more efficient hard sphere packing algorithm?

Using the Lubachevsky-Stillinger algorithm is the best choice. You get up to 64% space filling for a random monodisperse sphere packing. Another classical study is the algorithm by Jodrey and Tory (...
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### In Monte Carlo: does nonequilibrium imply stationary state?

No, nonequilibrium doesn't imply stationarity, but, at the sime time, using "nonequilibrium state" to denote those local energy minima can indeed be confusing, as it might seem to refer to ...
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### Is there a more efficient hard sphere packing algorithm?

For those looking for random packing, I suggest you look at https://github.com/VasiliBaranov/packing-generation (I am not affiliated). It supports the Lubachevsky–Stillinger, Jodrey–Tory, and force-...
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### How to simulate atomic scattering from solid walls at finite temperature for a particles in a box simulation?

Since no one has responded with expertise, I'll attempt a speculative answer here. To my mind, the simplest model of the atoms on the surface of the walls would be an ensemble of independent ...
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### Python script for Metropolis Monte Carlo (global optimisation)

A properly-run Metropolis Monte Carlo algorithm does not perform global optimisation. It returns the stationary distribution of a random process. In this case, you have specified an acceptance rule ...
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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 ...