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Questions tagged [free-energy]

Questions about free energy.

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20 votes
1 answer
674 views

What do phonon dispersion (or lattice dynamics) studies include?

I use the codes phonopy and phonopy-qha for phonon dispersion studies. phonopy-qha gives ...
Hitanshu Sachania's user avatar
19 votes
1 answer
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 ...
Achintha Ihalage's user avatar
14 votes
3 answers
236 views

What thermodynamic data is collected in order to build a CALPHAD model?

To build a model using the CALPHAD approach, i.e. Gibbs free energy as a function of composition and temperature, typically taking the form of a Redlich-Kister polynomial, what kind of thermodynamic ...
nathanielng's user avatar
13 votes
1 answer
426 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 ...
B. Kelly's user avatar
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12 votes
3 answers
487 views

Is there any definitive evidence that implicit solvation methods are more accurate than explicit solvation methods for free energy calculations?

I am looking for real data that concludes that implicit solvent models are definitively better than explicit solvent models for solvation free energy calculations. The motivation is a lovely reviewer ...
B. Kelly's user avatar
  • 4,376
12 votes
1 answer
218 views

What are the methods for calculating solvation effects in free energies and how do they compare?

I've just found this paper (J. Chem. Phys. 141, 174106 (2014)) that deals with the translational and rotational entropies in solution. The method is promising but, unfortunately, requires a ...
schneiderfelipe's user avatar
11 votes
1 answer
444 views

How to get order constitution data for single equilibrium calculation in Thermo-Calc's TC Python module?

I know that it is possible to get order constitution data for phases when using Thermo-Calc's GUI (e.g. to get "BCC_B2 DISORD" instead of just "BCC_B2") for a single equilibrium ...
sgp45's user avatar
  • 632
11 votes
0 answers
251 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) ...
fireball.1's user avatar
  • 1,083
10 votes
1 answer
252 views

Can I compute the free energy difference in (temporally) nearby micro-states using the Zwanzig equation for Free Energy Perturbation?

I wanted to understand the Free Energy Perturbation in an NVT ensemble. Wikipedia explains it as: $$ \tag{1} \Delta F = F_1 - F_0 = -\kappa T \ln \left<\exp\left( \frac{-(E_1-E_0)}{\kappa T}\right)...
fireball.1's user avatar
  • 1,083
10 votes
1 answer
188 views

Should one consider the spatial degeneracies of the electronic state while calculating the Gibbs free energy?

The Gibbs free energy of a molecule is generally expressed as a sum of translational, rotational, vibrational, electronic and nuclear contributions. The electronic contribution $G_{elec}$ is formally ...
wzkchem5's user avatar
  • 9,670
10 votes
1 answer
613 views

MM-GBSA from Induced Fit Docking on Maestro

How can an MM-GBSA(molecular mechanics energies combined with generalized Born and surface area continuum solvation) calculation be done from an induced fit docking (IFD) output? I performed an IFD ...
Giu's user avatar
  • 477
10 votes
0 answers
182 views

Single electron transfer periodic DFT in VASP [closed]

I have the following question: I am currently studying the electrocatalytic $\ce{CO2}$ reduction reaction (CO2RR) on $\ce{Cu}$ materials using periodic DFT calculations and I am using the ...
Jose Guillermo Rivera de la Cr's user avatar
9 votes
2 answers
701 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 ...
Alex I's user avatar
  • 1,038
9 votes
1 answer
2k views

How can we calculate the Gibbs free energy from first principles?

I am trying to calculate the Gibbs free energy for a bulk material. Since DFT ground state calculations give the energy at 0K, a temperature dependent part has to be added in this to obtain correct ...
Shahid Sattar's user avatar
9 votes
1 answer
237 views

VASP output energy

Which VASP output energy, after sigma -> 0 or before, do you use when combining with zero point energy and vibrational entropy obtained via vtst tools? (Vtst tools provide the vibrational frequencies ...
ericwalk's user avatar
  • 269
9 votes
1 answer
149 views

Water dimer and Free Energy Perturbation (FEP)

I am trying to understand FEP in the context of a water dimer. Let's say I want to calculate $\Delta A$, the free energy change for the following reaction: $$\ce{H_2O +H_2O\rightarrow H_2O-H_2O},\tag{...
user3001408's user avatar
9 votes
1 answer
469 views

For a Thermo-Calc database, is it possible to view the equation/parameters of the Gibbs free energy models?

I want to get the equations that model free energy for a given phase in a given alloy system (see attached image). I do not just want to get values of free energy for specific compositions. Is it ...
sgp45's user avatar
  • 632
9 votes
1 answer
341 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 ...
Hexagon Reversal's user avatar
8 votes
1 answer
906 views

Calculating enthalpy of a chemical reaction using DFT

Let's say we have a decomposition reaction $\tag{1}A \rightarrow B + C$ how would I go about calculating the Enthalpy of this chemical reaction using VASP. I am gonna describe what I am thinking below ...
Parmeet Singh EP 066's user avatar
7 votes
1 answer
389 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 ...
manuelpb's user avatar
  • 453
7 votes
1 answer
516 views

Thermo-Calc: how to suspend specific composition sets?

I am attempting to calculate the driving force of nucleation for several different precipitate phases using TC-Python. To this I want to suspend all phases, except for the matrix phase (e.g. FCC_L12). ...
sgp45's user avatar
  • 632
7 votes
1 answer
205 views

What information about a crystalline solid material goes into calculating phase diagrams in Thermo-Calc, and how?

Gibbs free energy, $G$, for a crystalline solid material could be described as: \begin{equation} G\: =\: H_{T=0}\: +\: H_{T>0}\: +\: \text{ZPE}\: -\: T\cdot S, \end{equation} Where $H$ is enthalpy, ...
Hitanshu Sachania's user avatar
6 votes
1 answer
572 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 ...
Nana Kofi Boakye's user avatar
6 votes
1 answer
132 views

Is it possible to analytically solve for a particular phase region of a CALPHAD database? (instead of guessing and checking)

As I understand it, a given CALPHAD database is essentially just a set of equations that model the Gibbs free energy of each phase within a given alloy system (set of elements). Typically, the main ...
sgp45's user avatar
  • 632
6 votes
1 answer
98 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 ...
BGK's user avatar
  • 61
6 votes
0 answers
117 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 ...
napadia's user avatar
  • 121
6 votes
0 answers
126 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 ...
napadia's user avatar
  • 121
6 votes
0 answers
747 views

How to calculate the Gibbs free energy for a reaction? [closed]

I am trying to learn how to calculate Gibbs free energy for a reaction. Assuming a reaction for two-dimensional TMDCs: MoS2 (solid) + 2Se(gas) ---> MoSe2 (solid)+ 2S (gas) I can calculate the ...
Shahid Sattar's user avatar
6 votes
0 answers
302 views

Why does Thermo-Calc one axis equilibrium calculation get stuck in never ending loop? [closed]

I've been trying to run a Thermo-Calc one axis equilibrium calculation on some quaternary alloys in the TCHEA4 database. Most of the calculations work fine, but for some alloys it gets stuck in a loop ...
sgp45's user avatar
  • 632
6 votes
1 answer
428 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 ...
sgp45's user avatar
  • 632
5 votes
3 answers
359 views

Gibbs free energy modification after finishing NEB?

I have finished the NEB calculation, but it seems all the energy I got is Internal energy instead of Gibbs free energy, so do I need to do Gibbs free energy modification? Is there any standard ...
Jack's user avatar
  • 2,057
5 votes
1 answer
177 views

Software for generating ensembles of dimer pairs of organic molecules

For two organic molecules of essentially unlimited size (up to and including, and sometimes exceeding MW = 1000 g/mol), I would like to generate all possible dimer pairs in vacuum. The pairs may be ...
Wesley's user avatar
  • 1,040
5 votes
1 answer
224 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 ...
sgp45's user avatar
  • 632
5 votes
1 answer
408 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 ...
Binh Thien's user avatar
  • 2,137
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 ...
이영규's user avatar
4 votes
1 answer
538 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 ...
leire's user avatar
  • 183
4 votes
0 answers
185 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 ...
erkoo's user avatar
  • 41
3 votes
0 answers
39 views

How to compute molar Gibbs free energy (chemical potential) for single molecule using gaussian09?

I want to calculate the Gibbs free energy of single gas molecule (AsH3) using Gaussian 09, but I am confused between "Thermal correction to Gibbs Free Energy" and "Sum of electronic and ...
Abhishek's user avatar
3 votes
0 answers
36 views

Proof that equilibrium phase fraction(s) is a continuous function of composition

It seems that the equilibrium phase fractions (i.e., relative amounts of phase A1, A2, ..., Aq for a system in which there are q total phases) as a function of composition (for a constant pressure and ...
sgp45's user avatar
  • 632
3 votes
0 answers
66 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 ...
P Teeuwen's user avatar
  • 131
3 votes
0 answers
826 views

What input setting in Quantum ESPRESSO will allow me to calculate the free energy of a solid? [closed]

I understand that it's possible to calculate the Gibbs free energy of a system ab initio, see for example: How can we calculate the Gibbs free energy from first principles? I'm wondering how I can do ...
Paulie Bao's user avatar
  • 3,973
2 votes
1 answer
103 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 ...
Alex I's user avatar
  • 1,038
2 votes
1 answer
56 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?
Nana Kofi Boakye's user avatar
2 votes
1 answer
127 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 ...
Manasi Vyas's user avatar
2 votes
0 answers
48 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 ...
Nana Kofi Boakye's user avatar
2 votes
0 answers
72 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 ...
ansonthms's user avatar
  • 991
1 vote
0 answers
117 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 ...
Robin's user avatar
  • 61