GROMACS implementation of free energy calculations with non-pairwise Variationally derived Intermediates

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...

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

GROMACS: Fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance...

Free Energy Simulations with Qm/mm Using Dftb3, Gromacs and Plumed

The approximative density-functional method DFTB3 has been implemented in the Gromacs package version 5, complementing the existing QM/MM interface. The tight integration within the program gives rise to favorable efficiency, and makes it possible to employ a full PME-based treatment of QM/MM electrostatic interaction. Therefore, unnecessary artifacts are avoided in simulations involving polar ...