New and improved features

Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface

Simulations of chemical reactions pathways can provide an atomistic insight into many biological and chemical processes. To perform such kind of modelling in complex systems, that includes solvent and/or proteins Multi-scale Quantum Mechanics / Molecular Mechanics (QM/MM) approaches are often used. Here we introduce a whole new interface to perform QM/MM simulations in fully periodic systems using MDModule that couples GROMACS with CP2K quantum chemistry package. This enables hybrid simulations of systems in systems where chemical reactions occurs. The interface supports most of the simulations techniques available in GROMACS including energy minimization, classical MD and enhanced sampling methods such as umbrella sampling and accelerated weight histogram method.

Transformation pull coordinate for mathematical transformations of pull coordinates

A new pull coordinate type named transformation has been added. This enables mathematical transformation of previously defined pull coordinates using a user supplied formula in a string. This allows for example non-linear transformation of a distance, e.g. a contact coordinate or (non-)linear combinations of multiple pull coordinates. This is a powerful tool for defining complex reaction coordinates and it can be combined with the Accelerated Weight Histogram Method to enhance sampling.

Replica-exchange molecular dynamics simulations with GPU update

Replica-exchange molecular dynamics now works with GPU update.

A new formulation of soft-core interactions for free energy calculations

With this addition Gromacs allows to choose from two schemes to soften non-bonded interactions during alchemical perturbations: Beutler et al.100 and Gapsys et al.185 soft-core functions.

More flexible sharing of biases in AWH

With the accelerated weight histogram method, biases can now be shared between subsets of all simulations, without restrictions. The allows for more flexible ensemble simulation setups, as well as simpler launches of sets of simulations.