# Questions tagged [free-energy]

33 questions
Filter by
Sorted by
Tagged with
47 views

### How to calculate Gibbs free energy of a reaction involving cations using GFN2-xTB (via ORCA)

I am trying to compare the Gibbs free energy of reactions such as: A + 4K(+) --> B(4+) A + 4Na(+) --> C(4+) A + 4Li(+) --> D(4+) A + 4Ca(2+) --> E(8+) A + 4Mg(2+) --> F(8+) In these ...
101 views

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

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
119 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
175 views

### Free energy as a function of temperature over phase transition in molecular dynamics simulation

I've constructed a low density standard MD simulation (in Python), using the Lennard-Jones potential with an Andersen thermostat, of 10 particles in a box V = 10 $\times$ 10 $\times$ 10 in the NVT ...
• 41
1 vote
44 views

### Free energy calculation

I want to plot the relationship between free energy and temperature. I want to consider two plots, when phonons are considered and when phonons are not considered how the free energy changes with ...
1 vote
91 views

### Free energy calculations for lammps

Is there any tutorial or reference available to perform free energy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; wisdom's particle insertion method) etc. with ...
• 11
47 views

### What is the best model to calculate the free energies using ASE thermochemistry?

I am trying to calculate the free energy of adsorption of a small molecule on a 2D material. After adsorption, I am using the thermochemistry module of the Atomic Simulation Environment to calculate ...
• 921
88 views

### Potential of mean force from potential energy

Imagine a simple model of a crystal where every atom in the crystal is the same, and the potential energy of the pairwise interaction between atoms is some radial function of distance, U = U(r). For ...
• 1,048
322 views

### Persistent errors in single equilibrium calculations (Thermo-Calc)

When running single point equilibrium calculations on an array of compositions I come across some compositions (for specific examples see below) that return the error ...
• 602
55 views

### What is the meaning of a "free energy per unit surface area" vs "pressure" plot?

I don't understand this graph. From the graph, does it mean that at high pressures the oxide layer is stable and this stability reduces at low pressures and temperatures?
450 views

### How to calculate Gibbs free energy of adsorption at constant temperature with varying pressures

I want to calculate the Gibbs free energy of adsorption for an oxidized surface. The literature I consulted used the equations attached to this post. I am trying hard to find my way through. Any idea ...
1 vote
35 views

### Adaptive Biasing Force Simulations in NAMD [closed]

I have performed an ABF simulation to investigate the binding of a small molecule with a 2D surface using NAMD. The initial simulation was for a scan window of 3 to 15 angstroms of z-projected ...
• 3,003
86 views

### What is the largest number of collective variables used in a metadynamics simulation?

Metadynamics is usually used to construct 1D or 2D free-energy surfaces. There seem to be a few examples for 3D free-energy surfaces: Paper 1: Exploring the Free Energy Landscape of Solutes Embedded ...
• 61
337 views

### Calculate deprotonation energy or Gibbs free energy of acids

I'm delving into the world of superacids, acids with an acid strength greater than that of sulfuric acid at 100%. I've recently encountered some computational papers which suggest that the ...
• 443
195 views

### How to calculate phase regions using CALPHAD for higher order systems (>3 elements)?

I primarily use Thermo-Calc so I will use that to describe my problem but I am interested to hear general CALPHAD insight as well. Using Thermo-Calc I can quickly get an idea of the phase regions ...
• 602
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 ...
• 51
256 views

### Zero point correction and free energy calculation with imaginary modes?

I am a beginner in DFT. Recently I have been working on calculating the energy (with zero point correction), and may be free energy in the future, for a structure in both stable and unstable ...
398 views

### How can I justify that in DFT entalphy is Gibbs free energy?

I am working in my final undergraduate Project about predicting belite (Ca2Si04) polymorphs using DFT calculations and I need to justify why my SIESTA run is looking for minimum enthalpy and not free ...
• 183
697 views

### Why are ions in water not paired?

This question is about ions in water, both in reality and as handled by MD (explicit solvent) and QM methods (eg AIMD). Basically the question is this: why are ions not always paired? For a back of ...
• 1,048
91 views

### Relationship between grand potential and free energy?

What is the fundamental relationship between grand potential and free energy? In other words, what assumptions need to be made in order to obtain the free energy equation rather than the grand ...
• 111
145 views

• 1,083
233 views

### Calculate free energy for a canonical (NVT) ensemble [closed]

Note: Users wishing to answer this question may write a comment or a message in the chat indicating their desire for the question to be re-opened. I have an NVT ensemble of water molecules (liquid) ...
• 1,083
2k views

### Difference between potential energy, free energy and Coulomb energy in solid state physics

I often encounter terms such as (Helmholtz, Gibbs) free energy, potential energy and total energy when describing the energy of a physical system at atomic level. Sometimes I stumble upon Coulomb ...
• 1,962