Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels.

The generalized master equation (GME) provides a powerful approach to study biomolecular dynamics via non-Markovian dynamic models built from molecular dynamics (MD) simulations. Previously, we have implemented the GME, namely the quasi Markov State Model (qMSM), where we explicitly calculate the memory kernel and propagate dynamics using a discretized GME. qMSM can be constructed with much shorter MD trajectories than the MSM.

EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules.

Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the expanded package for IET-based solvation (EPISOL), that performs 3D-reference interaction site model (3D-RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D-RISM theory, including the recent hydrophobicity-induced density inhomogeneity (HI) theory for hydrophobic solutes and ion-dipole correction (IDC) theory for negatively charged solutes.