Note: Free energy calculations for atomic solids through the Einstein crystal/molecule methodology using GROMACS and LAMMPS

Note: Free energy calculations for atomic solids through the Einstein crystal/molecule methodology using GROMACS and LAMMPS.

Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years seve...

A Python tool to set up relative free energy calculations in GROMACS

Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of findi...

Spherical self-consistent atomic deformation model for first-principles energy calculations in ionic crystalline solids.

We present a first-principles method @called spherical self-consistent atomic deformation ~SSCAD!# for calculating the energy per unit cell in ionic crystalline solids. SSCAD is a density-functional method using the local-density approximation ~LDA!. Wave functions are localized about each ion, resulting in a single-particle Schrödinger’s equation for each ion. To simplify the calculation, we s...

Revisiting the Frenkel-Ladd method to compute the free energy of solids: the Einstein molecule approach.

In this paper a new method to evaluate the free energy of solids is proposed. The method can be regarded as a variant of the method proposed by Frenkel and Ladd [J. Chem. Phys. 81, 3188 (1984)]. The main equations of the method can be derived in a simple way. The method can be easily implemented within a Monte Carlo program. We have applied the method to determine the free energy of hard sphere...