Questions tagged [statistical-thermodynamics]

Questions relating to the discipline of statistical thermodynamics.

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7
votes
1answer
50 views

For ergodicity, what is the significance of the R value and slope?

I am calculating MSDs for the first time and have been struggling to find newbie-level resources on understanding them. If anyone could please suggest any resources or provide guidance on how to ...
11
votes
1answer
65 views

Phonon density of states in statistical thermodynamics

Phonon density of states (DoS), $g_{(\omega_i)}$, help understand the distribution of states across frequencies of vibration. $\int g_{(\omega_i)}d\omega_i =$ the number of states between $\omega_i$ ...
3
votes
0answers
33 views

Deriving relations for a hard sphere phase diagram

In Torquato's Random Heterogeneous Materials, he has written $$\frac{p}{\rho kT} = 1+2^{d-1}\eta g_2 (D^{+})$$ where $g_2(D^+)$ is the contact value from the right-side of the radial distribution ...
6
votes
0answers
43 views

Evaluating $C_v$ for one mole $H_2$ molecules in a quantum simulation [closed]

Given an ensemble of $N$ diatomic molecules, we know that the rotational partition function is given by $$Z_r = z_r^N$$ where $$z_r = \sum_{l} (2l+1)e^{-Kl(l+1)}$$ where $K = \beta \hbar ^2 /2I$. I ...
18
votes
2answers
706 views

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 (...
7
votes
1answer
75 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 ...
15
votes
1answer
141 views

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 ...
8
votes
0answers
88 views

Coupling between 1st and 2nd order phase transitions?

I am seeking some models or references on how to couple, or what to take into consideration, while coupling first-order phase transitions (for magnetic systems) and second-order phase transitions, in ...
16
votes
3answers
443 views

References for Molecular Dynamics?

I am new to the world of Molecular Dynamics (zero practical experience), and I know that a starting point to really go into the back-bone of MD is Statistical Mechanics (took a semester course in ...
9
votes
0answers
78 views

I wrote a Python code to do MD for a Lennard-Jones fluid but the VACF is wrong: What might be the problem? [closed]

I am trying to write a molecular dynamics simulation for a Lennard-Jones fluid in a box with periodic boundary conditions. The box has no net momentum. I am writing this in python. I have written a ...
11
votes
2answers
114 views

Calculating diffusion coefficient from Mean Squared Displacement

I am performing a molecular dynamics simulation and I have calculated the velocity autocorrelation function (VACF), $\psi (t)$ and mean square displacement, $\langle (\Delta r)^2 \rangle$. In my ...
10
votes
1answer
157 views

Are there any MD packages that do proper free energy sampling in the NPT ensemble?

Statistical Mechanics is the basis of molecular level calculations of properties and averages. Nowadays free energy calculations are fairly "turn-the-crank", which is not necessarily a good ...
22
votes
1answer
116 views

How do you calculate the “true” chemical potential in classical density functional theory?

In classical density functional theory, one traditionally calculates the chemical potential by taking the variational derivative, \begin{equation} \mu_{i} = \frac{\delta F}{\delta \rho_{i}} \end{...
8
votes
1answer
65 views

What contributes to the total enthalpy of a system?

This answer refers to a paper that calculates $\Delta H$ as $\Delta E_{\textrm{electronic}} + \Delta E_{\textrm{vibrational}}$. However, what if I had enough computing power, and I wanted to get the ...