# Questions tagged [statistical-thermodynamics]

Questions relating to the discipline of statistical thermodynamics.

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### 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, \mu_{i} = \frac{\delta F}{\delta \rho_{i}}\tag{1} \...
809 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 (...
639 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 ...
168 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 ...
81 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 $\omega_i$ ...
396 views

### Which ensemble to use for a molecular dynamics simulation?

Does it matter which ensemble you use for a molecular dynamics simulation? Shouldn't they in principle give the same results? Why, historically, was it hard (and desirable) to develop simulations in ...
221 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 ...
98 views

### Selection of appropriate Langevin damping parameter for MD of solid metal

I am performing an MD simulation involving solid metal. The system is in the NVT ensemble, and I am using the Langevin thermostat (fix Langevin in LAMMPS) to enforce this. I have previously used the ...
174 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 ...
197 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 ...
456 views

### Why is specific heat not zero at absolute zero?

In this old paper on Monte Carlo simulations of Lennard-Jones solid, specific heat behaviour (both $c_p$ and $c_v$) have been reported. As you can see from the picture below, both $c_p$ and $c_v$ goes ...
99 views

### Coupling between 1st and 2nd order phase transitions? [closed]

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 ...
241 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 ...
79 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 ...
63 views

### Understanding the rigorous bridge between atomistic and coarse-grained simulations

I am currently reading this paper by Noid et. al. on the rigorous bridge between atomistic and coarse-grained simulations. In the paper, he defined a linear map from the atomistic coordinates and ...
76 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 ...
49 views