Simulations of electrosprayed proteins with FMM-enhanced GROMACS
Title: Simulations of electrosprayed proteins with FMM-enhanced GROMACS
DNr: NAISS 2024/22-641
Project Type: NAISS Small Compute
Principal Investigator: Louise Persson <>
Affiliation: Uppsala universitet
Duration: 2024-05-02 – 2025-06-01
Classification: 10602


A fast multipole method (FMM) for calculation of electrostatic interactions was recently implemented in the molecular dynamics software GROMACS, as an alternative to the commonly used particle mesh Ewald (PME) method. The attractiveness of FMM typically lies in its better scaling properties for highly parallel simulations, but in addition to this, it could be particularly beneficial for simulations of biomolecules in the gas phase, for two reasons: 1) FMM permits that systems are treated with open boundaries, instead of with periodic boundary conditions, which by construction is imperative with particle mesh Ewald method. This is a more realistic and accurate approach for gas-phase simulations. 2) It has been demonstrated that systems that are large and/or have inhomogeneous particle distribution benefit from significant performance enhancements with FMM. We will use GROMACS with FMM to simulate proteins under electrospray conditions. These systems are gaseous and highly charged, offering great opportunity for performance enhancements in addition to accurate treatment of boundaries. We hope to achieve particular speed-ups for large and highly charged protein complexes, simulations of which are currently severely restricted by low computational efficiency. Simulations of electrosprayed proteins are routinely performed to guide interpretation of experimental data from mass spectrometry measurements. Our research group also uses simulations of this kind to inform in the development of new mass spectrometric techniques.