Improved Sampling for Biological Molecules Using Shadow Hybrid Monte Carlo

Shadow Hybrid Monte Carlo (SHMC) is a new method for sampling the phase space of large biological molecules. It improves sampling by allowing larger time steps and system sizes in the molecular dynamics (MD) step of Hybrid Monte Carlo (HMC). This is achieved by sampling from high order approximations to the modified Hamiltonian, which is exactly integrated by a symplectic MD integrator. SHMC requires extra storage, modest computational overhead, and a reweighting step to obtain averages from the canonical ensemble. Numerical experiments are performed on biological molecules, ranging from a small peptide with 66 atoms to a large solvated protein with 14281 atoms. Experimentally, SHMC achieves an order magnitude speedup in sampling efficiency for medium sized proteins.

• Type: Conference
• Year: 2004
• Where: ICCS
• Authors: Scott S. Hampton, Jesús A. Izaguirre
• Keywords: Biological Molecules, Hybrid Monte Carlo, ICCS 2004, Large Biological Molecules