The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels

KLEIN, FLORENCIA; SOÑORA, MARTÍN; HELENE SANTOS, LUCIANNA; FRIGINI, EZEQUIEL N; BALLESTEROS-CASALLAS, ANDRÉS; RODRIGO MACHADO, MATÍAS; PANTANO, SERGIO

JOURNAL OF STRUCTURAL BIOLOGY

ACADEMIC PRESS INC ELSEVIER SCIENCE

Año: 2023

1047-8477

The different combinations of molecular dynamics simulations with coarse-grained representations have acquired considerable popularity among the scientific community. Especially in biocomputing, the significant speedup granted by simplified molecular models opened the possibility of increasing the diversity and complexity of macromolecular systems, providing realistic insights on large assemblies for more extended time windows.However, a holistic view of biological ensembles´ structural and dynamic features requires a self-consistent force field, namely, a set of equations and parameters that describe the intra and intermolecular interactions among moieties of diverse chemical nature (i.e., nucleic and amino acids, lipids, solvent, ions, etc.). Nevertheless, examples of such force fields are scarce in the literature at the fully atomistic and coarse-grained levels. Moreover, the number of force fields capable of handling simultaneously different scales is restricted to a handful. Among those, the SIRAH force field, developed in our group, furnishes a set of topologies and tools that facilitate the setting up and running of molecular dynamics simulations at the coarse-grained and multiscale levels. SIRAH uses the same classical pairwise Hamiltonian function implemented in the most popular molecular dynamics software. In particular, it runs natively in AMBER and Gromacs engines, and porting it to other simulation packages is straightforward.This review describes the underlying philosophy behind the development of SIRAH over the years and across families of biological molecules, discussing current limitations and future implementations.