MSC 2000 Seminar: Thursday, 23 March 2000, 1:40 pm

Solvation in Molecular Dynamics and Quantum Chemistry

Daniel T. Mainz & William A. Goddard III

Materials and Process Simulation Center, Caltech, Pasadena, CA 91125


Solvation effects are of tremendous importance to molecular simulation, and are a primary research concern at the MSC, where several collaborators are studying peptide folding statistics, novel dendritic polymer structures and functionalities, and developing new force fields based on quantum chemistry results in solution. Discussed along with the key simulation programs in development by our group, including Jaguar (QM) and MPSim (parallel MD), several methods to include solvation will be addressed. Of these, continuum dielectric methods best balance the competing needs for acceptable accuracy and computational efficiency. The use of the Poisson-Boltzmann equation for solvation is presented, and serves as the foundation for computational packages which use finite element approaches (PBF) and Generalized Born (GB) algorithms. PBF works exceptionally well with ab initio programs, yielding solvation free energies within 0.4 kcal/mol at little additional cost to a gas-phase calculation. Because it is a faster algorithm, GB methods are a better fit for molecular dynamics simulations. The S-GB program significantly improves upon the GB formulation; in addition to being faster and scaling better with system size, it is especially amenable to computational parallelization; this shall bring solvated dynamical simulations with MPSim to be only marginally more expensive than solute-only calculations. Finally, methods to bring quantum mechanics, molecular mechanics, and continuum solvation together in complex QM/MM simulations will be discussed. These calculations, presently underway, are the beginnings of true hierarchical simulation methods of significant importance to the MSC's research purposes.



Figure 1: Parallel scaling of MPSim on a half-million atom structure of a common rhinovirus using SGI Origin2000 machines up to 64 processors. The red line shows the inferior scaling of level 5 octree decomposition, compared to the blue line's scaling of level 6 decomposition.

Figure 2: QM/MM schematic for calculating condensed-phase structures, vibrational frequencies, and relative energies of minimum and transition state structures of RDX, a high-explosive. The green atoms are calculated with Jaguar, the others with IMPACT or MPSim, and all the atoms are surrounded by a continuum solvent evaluated with PBF.