Poisson−Boltzmann Analytical Gradients for Molecular Modeling Calculations

Abstract

We present the first analytical gradient Poisson−Boltzmann methodology which is routinely applicable to large biomolecular systems, such as proteins with sizes ranging from 500 to 5000 atoms. Full minimizations of several such systems in the gas phase and in solution are contrasted. Because the solvation free energy term is slowly varying with conformation, it can be evaluated infrequently in the simulation, and hence, reasonable computation times can be obtained even for large solvated systems.