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 ...
14
votes
Accepted
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 ...
14
votes
Accepted
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
...
13
votes
Accepted
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 ...
13
votes
Accepted
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 ...
12
votes
Accepted
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 $\...
11
votes
Accepted
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 ...
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 ...
10
votes
Accepted
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 ...
10
votes
Accepted
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 ...
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 ...
10
votes
Accepted
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 ...
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 ...
9
votes
Accepted
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. ...
9
votes
Accepted
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 ...
9
votes
Accepted
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 ...
9
votes
How to choose between Molecular Dynamics and Monte Carlo when beginning to simulate either equilibrium or non-equilibrium systems?
The main difference between MD and MC is, MD is a deterministic method, and MC is a probabilistic method.
So, MC is unable to simulate something which needs total accuracy. For instance, if you want ...
8
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 ...
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 ...
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 ...
8
votes
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 ...
8
votes
Is converting values from reduced units to physical units a good idea?
When comparing a molecular simulation to one type of physical material, it does not matter whether the computer program has used "reduced units" or "real units".
The computer ...
7
votes
Accepted
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 ...
7
votes
Accepted
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, ...
7
votes
Are MD and MC both able to study both equilibrium and non-equilibrium systems?
Monte Carlo methods such as FCIQMC can study non-equilibrium systems: in fact FCIQMC is used for calculating the ground state energy of a system that is already in equilibrium.
Monte Carlo methods can ...
7
votes
Accepted
Are MD and MC both parts of statistical physics?
Monte Carlo methods are a broad class of algorithms that apply not just to physics problems but also to biology, finance, and even pure mathematics (for example it can be used to provide better and ...
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 ...
6
votes
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-...
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 (...
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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