CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides

Hydrogen mass repartitioning (HMR) that permits time steps of all-atom molecular dynamics simulation up to 4 fs by increasing the hydrogen atoms has been used in protein and phospholipid bilayers simulations improve conformational sampling. Molecular input generation via CHARMM-GUI now supports HMR for diverse programs. In addition, considering ambiguous pH at bacterial outer membrane surface, different protonation states, either -2e or -1e, phosphate groups lipopolysaccharides (LPS) are also supported LPS Modeler. To examine robustness influence states on bilayer properties, eight LPS-type systems with two modeled simulated utilizing both OpenMM 2-fs (standard) 4-fs schemes. Consistency space sampled standard shows reliability even LPS, one most complex biomolecules. For similar conformations a PO41- PO42- group, but make slight impacts lipid packing properties acyl chains. Systems have slightly smaller area per thus more ordered A chains compared those PO42-, due electrostatic repulsion between neutralizing Ca2+ ions. phosphates available expected be useful further investigations biological origin.