Modeling DMPC lipid membranes with SIRAH force-field

FRIGINI, EZEQUIEL N.; PORASSO, RODOLFO D.; BARRERA, EXEQUIEL E.; PANTANO, SERGIO

JOURNAL OF MOLECULAR MODELING - (Print)

SPRINGER

Lugar: Berlin; Año: 2017 vol. 23 p. 259 - 264

1610-2940

Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations (http://www.sirahff.com). We show that the present model not only achieves a correct reproduction of structural parameters as area per lipid andthickness, but also dynamic descriptors such as diffusion coefficient, order parameters, and proper temperature driven variations. Adding phospholipid membranes to the existing aqueous solution, protein and DNA representations of the SIRAH force field permit considering the most common problems tackled by the biomolecular simulation community.