CONSTRAINT DYNAMICS ALGORITHM FOR SIMULATION OF SEMIFLEXIBLE MACROMOLECULES

Semiflexible models are often used to study macromolecules containing stable structural elements. Based on rigid body dynamics, we developed a rigid fragment constraint dynamics algorithm for the simulation of semiflexible macromolecules. Stable structural elements are treated as rigid fragments. Rigid fragment constraints, defined as combinations of distance constraints and position constraints, are introduced to li mit internal molecular motion to the required mode. The constraint for ces are solved separately for each rigid fragment constraint and itera tively until all constraint conditions are satisfied within a given to lerance at each time step, as is done for the bond length constraint i n the SHAKE algorithm. The orientation of a rigid fragment is represen ted by the quaternion parameters, and both translation and rotation ar e solved by the leap-frog formulation. We tested the algorithm with mo lecular dynamics simulations of a series of peptides and a small prote in. The computation cost for the constraints is roughly proportional t o the size of the molecule. In the microcanonical ensemble simulation of polyvalines, the total energy was conserved satisfactorily with tim e steps as large as 20 fs. A helix folding simulation of a synthetic p eptide was carried out to show the efficiency of the algorithm in a co nformational search. (C) 1998 John Wiley & Sons, Inc.