Compatibility of GROMOS-Derived Atomic Parameters for Lipopolysaccharide Membranes with the SPC/E Water Model and Alternative Long-Range Electrostatic Treatments Using Single Nonbonded Cutoff and Atom-Based Charge Schemes

• Autor(a) principal: Lima,Manoela P. M.
• Data de Publicação: 2019
• Outros Autores: Nader,Manuela, Santos,Denys E. S., Soares,Thereza A.
• Tipo de documento: Artigo
• Idioma: eng
• Título da fonte: Journal of the Brazilian Chemical Society (Online)
• Texto Completo: http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0103-50532019001002219
• topic: atom-based charge truncation; reaction field approximation; particle mesh Ewald; single cutoff; Verlet algorithm; GROMACS v.2106; bacterial outer membrane

Recent developments of GROMACS v.2016 ceased to support methodological approaches used in the development and validation of the GROMOS force field. We investigated the performance of a previously developed extension of the GROMOS force field for lipopolysaccharides to reproduce the structural dynamics of bacterial outer membrane (OM) using a single cutoff for nonbonded interactions and atom-based charge truncation. We further compared this setup for use with reaction field (RF) or particle mesh Ewald (PME) approximations in the presence of simple point charge (SPC) and extended simple point charge (SPC/E) water models. We find that the OM structural dynamics is well conserved in all simulated conditions, reproducing the available experimental data within the measurement uncertainty. The SPC/E model induces a small increase in OM fluidity, and when combined with the RF correction, shows a decrease in water orientation at the membrane surface. The present simulations support the compatibility of the GROMOS-derived lipopolysaccharide (LPS) parameters for use with single cutoff and atom-based charge schemes, either with RF or PME approximations, in GROMACS v.2016. Both SPC and SPC/E water models are suitable for use, but usage of SPC/E combined with the reaction field correction needs to be further investigated.