Incorporation of the magnetic field in GROMACS: validation and applications in biological systems

Abstract

The field of magnetobiology is garnering increasing interest due to its significant contributions across various disciplines, including biotechnology, medicine, and agriculture. Despite experimental evidence indicating the impact of magnetic fields on living organisms, the precise molecular-level effects of these fields remain unclear. Experimental studies of these phenomena at the molecular scale present significant challenges. In this regard, contributions from physics and theoretical chemistry are particularly relevant. However, the computational methodologies developed thus far are unable to incorporate magnetic fields into complex systems such as membrane proteins or biomolecules. In this context, the present work integrates the homogeneous magnetic flux density (B) term into the Verlet velocity algorithm implemented in the GROMACS package. This modification enables molecular dynamics simulations for such systems under the influence of a magnetic field. The implementation has been validated using two model systems: a free ion exposed to B ranging from 80 kT to 1500 kT, and a water box exposed to B between 0 T and 10 T. Furthermore, the stability of a protein was tested under the influence of B ranging from 0 T to 10 kT. The results demonstrated that the systems behaved in accordance with both theoretical and experimental expectations, thereby validating the modification of the algorithm and paving the way for future applications.