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# Questions tagged [statistical-thermodynamics]

Questions relating to the discipline of statistical thermodynamics.

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2 votes
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### energy fluctuations in NVE ensemble in molecular dynamics

One can check if the timestep used in molecular dynamics is small enough by looking at the energy conservation in a NVE simulation. From what I understand, due to errors in the integrator (for the ...
3 votes
0 answers
55 views

### Very high pressure fluctuations in molecular dynamics

I'm performing molecular dynamics simulations through the TIP3F model for water in NpT ensemble. The pressure control is attained by using the bussi barostat, while the temperature one through the ...
4 votes
1 answer
44 views

### phase average uncertainty in molecular dynamics

I was wondering if I could find some scaling relation of the uncertainity of phase averages of thermodynamic quantities with the number of atoms $N_a$, the number of timesteps $N_t$ and size of the ...
• 41
6 votes
0 answers
121 views

### Why is potential energy used and not total energy when calculating free energy? [closed]

I have run a replica-exchange molecular dynamics simulation, using a number, $n$, of replicas initiated at the same number, $n$, of unique temperatures. I have calculated the free energy profile over ...
• 121
3 votes
1 answer
249 views

### Thermal Properties Calculated with Phonopy

In Phonopy the thermal properties, free energy, heat capacity, and entropy, are calculated from their statistical thermodynamic expressions using phonon frequencies on a sampling mesh in the ...
• 3,500
6 votes
0 answers
129 views

### Free energy calculation as a function of temperature over phase transition

I've run a molecular dynamics simulation (NVT) of a simple Lennard-Jones system of a few particles and I'm trying to calculate the Helmholtz free energy $\Delta F$ as a function of temperature over ...
• 121
4 votes
2 answers
257 views

### 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 ...
• 2,556
4 votes
1 answer
141 views

### 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?
• 2,556
9 votes
1 answer
359 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 ...
• 2,556
5 votes
1 answer
140 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 ...
5 votes
1 answer
101 views

### How to apply solvent-correction to Gaussian derived Gibbs energies?

I study reaction A + B ā 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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5 votes
0 answers
38 views

### 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 ...
4 votes
1 answer
84 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 ...
• 4,181
6 votes
0 answers
57 views

• 317
4 votes
1 answer
252 views

### 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 ...
4 votes
0 answers
122 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 ...
• 4,181
5 votes
1 answer
427 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 ...
• 2,197
7 votes
1 answer
250 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 ...
• 2,352
9 votes
1 answer
379 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 ...
6 votes
1 answer
100 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 ...
• 4,181
9 votes
1 answer
141 views

• 4,181