POMsDB

This is POMsDB, an open and freely accessible database of quantum-chemically optimized molecular structures and force field (FF) parameters of POMs to run molecular dynamic (MD) simulations in common MD programs.

FF parameters are generated with our automated code polytype¹. Polytype enables the assignment of unique atom type for each atom, whereas at same time classify oxygen atoms of POM as terminal, bonding, and central ones, strongly useful for visualization and trajectory analysis. FF parameters of this database consist of atomic point charges, Lennard-Jones (LJ) parameters, and equilibrium-bonded parameters. Three different type of DFT atomic charges and two sets of LJ parameters could be selected. In addition, two different definitions of bonding intramolecular parameters are allowed, the standard used in previous POMs’ MD studies² whereas POM behaves as a rigid molecule (Frozen-polytype) and new approach based on modified Seminario method³ (ModSem-polytype), whereas POM behaves as a flexible molecule leading intra-molecular coordinates of POM to move along the dynamics.