Evaluation of all-atom force fields in viral capsid simulations and properties

Abstract

As the past century has been characterized by waves of viral pandemics, there is an ever-growing role for molecular simulation-based research. In this study, we utilize all-atom molecular dynamics to simulate an enterovirus-D68 capsid and examine the dependency of viral capsid dynamics and properties on AMBER and CHARMM force fields. Out of the six force fields studied, we note that CHARMM36m and CHARMM36 generate secondary structures that are most consistent with protein structural data and sample the largest conformational space. The ion distribution and radius of gyration of the capsid are similar across all force fields investigated.