Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function.
A symplectic multiple-time-step (MTS) algorithm has been developed for the united-residue (UNRES) force field. In this algorithm, the slow-varying forces (which contain most of the long-range interactions and are, therefore, expensive to compute) are integrated with a larger time step, termed the basic time step, and the fast-varying forces are integrated with a shorter time step, which is an integral fraction of the basic time step. Based on the split operator formalism, the equations of motion were derived. Separation of the fast- and slow-varying forces leads to stable molecular dynamics with longer time steps. The algorithms were tested with the Ala(10) polypeptide chain and two versions of the UNRES force field: the current one in which the energy components accounting for the energetics of side-chain rotamers (U(rot)) can lead to numerically unstable forces and a modified one in which the the present U(rot) was replaced by a numerically stable expression which, at present, is parametrized only for polyalanine chains. With the modified UNRES potential, stable trajectories were obtained even when extending the basic time step to 15 fs and, with the original UNRES potentials, the basic time step is 1 fs. An adaptive multiple-time-step (A-MTS) algorithm is proposed to handle instabilities in the forces; in this method, the number of substeps in the basic time step varies depending on the change of the magnitude of the acceleration. With this algorithm, the basic time step is 1 fs but the number of substeps and, consequently, the computational cost are reduced with respect to the MTS algorithm. The use of the UNRES mesoscopic energy function and the algorithms derived in this work enables one to increase the simulation time period by several orders of magnitude compared to conventional atomic-resolution molecular dynamics approaches and, consequently, such an approach appears applicable to simulating protein-folding pathways, protein functional dynamics in a real molecular environment, and dynamical molecular recognition processes.
Rakowski
Franciszek
F
Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego Street 5a, 02-106 Warsaw, Poland.
Grochowski
Paweł
P
Lesyng
Bogdan
B
Liwo
Adam
A
Scheraga
Harold A
HA
D000465:Algorithms; D003198:Computer Simulation; D004735:Energy Transfer; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D011506:Proteins / Q000737:chemistry*; D013314:Stress, Mechanical
D011506:Proteins