Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations

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...

Gamma-point lattice free energy estimates from O1 force calculations.

We present a new method for estimating the vibrational free energy of crystal (and molecular) structures employing only a single force calculation, for a particularly displaced configuration, in addition to the calculation of the ground state configuration. This displacement vector is the sum of the phonon eigenvectors obtained from a fast-relative to, e.g., density-functional theory (DFT)-Hess...

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

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

Quantitative free energy computation involves both using a model that is sufficiently faithful to the experimental system under study ~accuracy! and establishing statistically meaningful measures of the uncertainties resulting from finite sampling ~precision!. We use large-scale distributed computing to access sufficient computational resources to extensively sample molecular systems and thus r...