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# Matter Modeling : Recent Questions and Answers (Page 2)

## Why am I losing bonds when I use PACKMOL on two proteins?

I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code:tolerance 3.0filetype pdboutput E_S.pdbstructure E.pdb number 1 inside box...

## Can we "invert" Density Functional Theory through sufficiently accurate experiment?

The famous Hohenberg-Kohn theorems say that there is a one-to-one mapping between the many-body Hamiltonian, $mathcal{H}$, of a solid and its ground-state electron density $rho(mathbf{r})$. As far as...

## 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}}tag{1}end{equation}of the Helmholtz free energy...

## Converging the potential of a dilute binary alloy system using the Coherent Potential Approximation. What troubleshooting options could I take?

I'm trying to converge a dilute fcc alloy consisting of Cu and U, with the Uranium concentration at 0.01% and the lattice parameter of Cu, using Hubert Ebert's Spin Polarized...

## The Hund's J - Why can this be quantified?

I was reading on the implementation of Hubbard 'U' in Density Functional Theory. The Hubbard 'U' can be thought of as a parameter that accounts for the on-site electron-electron interactions...

## How accurate are the most accurate calculations?

Taking into account the fact that the theory of quantum gravity does not exist and the QED calculations are not possible for most realistic chemical systems, what levels of accuracy...

Asked on 12/13/2021 by Roman Korol

## Is there any software that can generate the electronic DOS of GaAs?

I want to calculate the density of states of GaAs conduction band (preferably each valley like Gamma, L and X). Is there any software available where I can easily generate...

## Which Linux distribution is best for Matter Modeling?

In some science fields there are efforts to provide customized distributions, so you can get a productive environment with minimum set-up overhead. For example, in high energy particle physics, we...

## What is the role of a chemist in computational chemistry?

As someone that wants to learn about computational chemistry, mainly for its use in energy storage materials (and therefore DFT as the most practical method of it), I am...

Asked on 12/09/2021 by Georgios Karaiskakis

## How to deduce phase transitions from a phonon calculation?

I came across the concept of using phonons to establish a material's dynamical stability, based on whether or not imaginary frequencies are present in its phonon band structure. What I...