A multiscale model for efficient simulation of a membrane bound viral fusion peptide

Biomolecular simulations have been particularly useful in providing atomic-level insights into biological processes. The simulations can be conducted at atomistic or coarse-grained resolution. An atomistic simulation can model atomic details of a biological process but is computationally expensive. A coarse-grained simulation is time-efficient but cannot fully expose atomic details. In order to support efficient simulations of complex biomolecular processes, we have developed a multiscale simulation model that dynamically integrates both atomistic and coarse-grained simulations. The model has been used to simulate a membrane bound viral fusion peptide associating with a phospholipid bilayer. The simulation provides an important pre-requisite in understanding the viral fusion mechanism that can aid the design of better drugs against infectious viruses. The simulation has achieved a high performance with a minimum 8-fold speedup. © 2007 IEEE.