# Questions tagged [statistical-thermodynamics]

Questions relating to the discipline of statistical thermodynamics.

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### Thermodynamics: System versus Ensemble

In the context of thermodynamics, an ensemble is a hypothetical collection of identical copies of a system, each in a different state, used to represent the statistical behavior of the system. That ...
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### Are MD and MC both parts of statistical physics?

Are MD (Molecular Dynamics) and MC (Monte Carlo) both parts of statistical physics or is only one of them? If so, which branch (e.g., mechanics, thermodynamics, etc.) and why?
276 views

### Difference between Statistical Physics, Statistical Mechanics, and Molecular Modeling?

I am looking for relevant books to study the modeling and Monte Carlo simulation of protein chains. I see that books related to Statistical Physics, Statistical Mechanics, and Molecular Modeling have ...
122 views

### gyration radius of short freely jointed chain with excluded volume

The freely jointed chain model without excluded volume has the following gyration radius, $$\langle R_g^2 \rangle=\frac{1}{6}\frac{N+2}{N+1}Na^2$$ where $N$ is the number of bonds and $a$ their ...
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### How to apply solvent-correction to Gaussian derived Gibbs energies?

I study reaction A + B → C + D in a water using DFT. I think I should apply some kind of correction over RRHO because it is not true in a solvent. I found the given work (https://doi.org/10.1021/...
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### How to get statistical temperature from WHAM? [closed]

I ran a series of replica exchange molecular dynmaics for the different temperatures. I used WHAM to sample metastable states. From the results of WHAM, we can get probabilties ($p$) from the energy ...
82 views

### Why does the 𝛿 (delta) term exist in the density-density correlation for simple liquids?

Cross-posted from the PhysicsSE. I am reading Theory of Simple Liquids by Hansen and McDonald, and they in chapter 3, they describe the density-density correlation for a simple liquid in the grand ...
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### How to assign a "Boltzmann weight"?

I would like to assign a "Boltzmann weight" i.e. $\exp(-E/kT)$ to interactions between particles based on the relative energies. But wouldn't the largest particle-particle energies have the ... 71 views

### Statistical properties of semi-flexible polymers

I am reading Statistical Physics of Particles by Kardar. I am struggling with problem 12d, in chapter 2, about semi-flexible polymers in two dimensions. The problem is as follows: Configurations of a ...
349 views

### How to estimate chemical potential at a temperature?

Fermi level is electron chemical potential at 0K and we can obtain it from DFT calculation. However, the chemical potential is dependent on temperature. But I only find the equation for gas or simple ...
206 views

### Is it incorrect to use a NVT ensemble for Non-equilibrium MD simulation?

I am getting some conflicting results on this topic while searching for literature online, so I am asking this question here with respect to a simplified experimental setup. If we are trying to ...
308 views

### How do you calculate a radial distribution function on a lattice?

For the radial distribution function $$g(r)=\frac{N(r)}{4\pi r^{2}dr \rho}$$ how do you do the calculation of the volume of the spherical shell in the denominator, $4\pi r^{2} dr$, when the simulation ... 87 views

### 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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### Why do people care about reversibility in molecular dynamics simulations?

When carrying out a molecular dynamics simulation, one has to choose an ensemble. Depending on the problem, one usually works in the microcanonical (NVE), canonical (NVT), or grand canonical ensemble (...
929 views

### Algorithm for calculating dielectric constant of water TIP3P

I am running a NVT TIP3P simulation of water with 125 molecules of water in a 16-by-16-16 angstrom box with periodic boundary conditions on LAMMPS, with a time-step of 1 fs for 10 ps. Once the ...
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### Is there any reason not to sum the kinetic and potential energy from an NPT simulation to get internal energy?

I would be very grateful for some newbie-level advice from a thermodynamics guru. I ran NPT simulations on a particular system (in CP2K software) to get fluid densities for use in fluid dynamics ...