Implementing Dimer Metadynamics using GROMACS

TL;DR

This paper presents a GROMACS implementation of Dimer Metadynamics, enabling enhanced sampling in molecular simulations through a custom collective variable, with demonstrated efficiency and consistency across different peptide systems.

Contribution

The authors developed a GROMACS-based implementation of Dimer Metadynamics using a Plumed collective variable, improving sampling efficiency and compatibility with existing simulation workflows.

Findings

Implementation is consistent with standard methods.

Results are smoother and require shorter simulations.

Effective for peptide systems in vacuum and water.

Abstract

We develop a Gromacs implementation of Dimer Metadynamics[JCTC 13, 425 (2017)] for enhanced sampling through artificial delocalization effects. This implementation is based entirely on a Plumed collective variable developed for this purpose, the fine tuning of Gromacs input parameters, modified forcefields and custom non-bonded interactions. We demonstrate this implementation on Alanine Dipeptide in vacuum and in water, and on the 12-residue Alanine Polypeptide in water and compare the results with a standard multiple-replica technique such as Parallel Tempering. In all the considered cases this comparison is consistent and the results with Dimer Metadynamics are smoother and require shorter simulations, thus proving the consistency and effectiveness of this Gromacs implementation.