14 votes

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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  • 7,223
14 votes
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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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14 votes
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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 \begin{equation} F = C - P + 2 ...
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  • 4,066
13 votes
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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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  • 246
13 votes
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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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12 votes
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Are there examples of ab initio predictions on small molecules without the "major approximations"?

I wrote an answer to a similar question in the past, but focused in that question only on the state-of-the-art ultra-high precision calculations on atoms and the three most common isotopologues of $\...
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11 votes
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How do you incorporate hydrogen bonding into molecular simulations?

The current biomolecular force fields that I'm familiar with don't include any special energy terms for hydrogen bonds. Typically, hydrogen atoms that are capable of hydrogen bonding have very small ...
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11 votes

What are the types of Quantum Monte Carlo?

DMC (Diffusion Monte Carlo) Theory. Consider the Schrödinger equation in imaginary time $\tau=it$: $$ -\hbar\frac{\partial\psi(x,\tau)}{\partial\tau}=\hat{H}\psi(x,\tau). $$ For a time-independent ...
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10 votes

What are the types of Quantum Monte Carlo?

FN-DMC (Fixed-node diffusion Monte Carlo) Theory. See my answer about DMC. The only addition for FN-DMC is that the ground state of an arbitrary Hamiltonian will not be antisymmetrized, and therefore ...
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10 votes

Starting configuration for a molecular simulation

All depends on what are you working on. When doing a computer simulation, what’s the best way to prepare a starting configuration to avoid biasing your results? If working with molecules in gas ...
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10 votes
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Autocorrelation function problem in Monte Carlo simulation of 2D Ising model

First, some general remarks: The measurements should be made after the system has equilibrated, i.e., a large number of the first iterations should be discarded before the analysis. They should also ...
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10 votes
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How can very small lattices be sufficient for Quantum Monte Carlo simulations?

I think you are correct that there is an aspect of "take what you can get" to the sizes that are typically used in numerical methods. Even with finite size scaling (FSS), you usually try to go to the ...
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9 votes
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Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance

Most of the problem here appears to be because constraints in the test system default to app.HBonds, which means all bonds to hydrogen atoms are constrained. ...
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  • 1,887
9 votes
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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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9 votes
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Why is specific heat not zero at absolute zero?

You are correct that this is due to not including quantum effects. Ref 1 in your figure is the paper cited below. In this paper, they explicitly mention that $C_v$ calculated using the cell-cluster ...
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8 votes
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Is there a more efficient hard sphere packing algorithm?

If you want faster solution, you can use simplification. If there are more than some critical amount of spheres (about 100), then grid solution is likely almost as good as true solution. Make a ...
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8 votes

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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  • 4,066
8 votes

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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7 votes

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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  • 171
7 votes
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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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7 votes
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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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6 votes

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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  • 1,030
6 votes

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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  • 161
6 votes

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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  • 786
5 votes

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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4 votes

Starting configuration for a molecular simulation

In order to perform a molecular dynamics simulation, you need to equilibrate the system before you can get good statistics. In principle, you can use any starting point, since the simulation should be ...
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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 ...
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  • 613
3 votes
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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 $\...
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  • 4,066
3 votes
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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 ...
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  • 613
3 votes

Simulating polymers using cellular automata?

Eventually, the question should be more detailed. However, for starters and in general, I would start by giving a cursory read to any wide piece of work that contains this problem, in order to get ...
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