Computer simulation of solid C60 using multiple time-step algorithms

Procacci, Piero; Berne, B. J.
August 1994
Journal of Chemical Physics;8/1/1994, Vol. 101 Issue 3, p2421
Academic Journal
The reversible reference system propagator algorithm (r-RESPA), based on a Trotter factorization of the classical propagator, is tested in a molecular dynamics simulation of solid C60. We show how, with an appropriate subdivision of the interaction potential and with a careful balancing of the integration parameters, one can adopt large time steps and impressively efficient r-RESPA integrators which yield the same dynamics obtained by means of the small time-step Verlet algorithm. The results presented here show that the use of r-RESPA integrators speeds up the simulation by a factor of between 20–40 with respect to the standard Verlet algorithms.


Related Articles

  • Spatially local parallel tempering for thermal-equilibrium sampling. Spinney, R. E.; Bowler, D. R.; Gillan, M. J. // Journal of Chemical Physics;3/14/2010, Vol. 132 Issue 10, p104106 

    Parallel tempering (PT) is a set of techniques for accelerating thermal-equilibrium sampling in systems where the exploration of configuration space is hindered by energy barriers. With standard PT algorithms, the computational effort scales unfavorably with system size, so that it is difficult...

  • Molecular dynamics simulations and drug discovery.  // BMC Biology;2011, Vol. 9 Issue 1, p71 

    The article cites a research study that examines the roles atomistic computer simulations of macromolecular receptors and their associated small-molecule ligands can play in drug discovery. It discusses the limitations of simulation methodologies applicable today. It was found that the future of...

  • Trajectory NG: portable, compressed, general molecular dynamics trajectories. Spångberg, Daniel; Larsson, Daniel; Spoel, David // Journal of Molecular Modeling;Oct2011, Vol. 17 Issue 10, p2669 

    We present general algorithms for the compression of molecular dynamics trajectories. The standard ways to store MD trajectories as text or as raw binary floating point numbers result in very large files when efficient simulation programs are used on supercomputers. Our algorithms are based on...

  • Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency. Han Wang; Dommert, Florian; Holm, Christian // Journal of Chemical Physics;7/21/2010, Vol. 133 Issue 3, p034117 

    We construct an accurate error estimate for the root mean square force error of the smooth particle mesh Ewald (SPME) algorithm, which is often used for molecular dynamics simulations, where charge configurations under periodic boundary conditions require considerable amounts of CPU time. The...

  • Communication: Simulated tempering with fast on-the-fly weight determination. Nguyen, Phuong H.; Okamoto, Yuko; Derreumaux, Philippe // Journal of Chemical Physics;2/14/2013, Vol. 138 Issue 6, p061102 

    We propose an efficient method to enhance sampling in computer simulations by combining the simulated tempering algorithm with a fast on-the-fly weight determination scheme. The weights are self-updated via a trapezoid rule during the simulated tempering simulation. With our proposed scheme,...

  • On Computational Strategies within Molecular Dynamics Simulation. Sergi, Alessandro; Giaquinta, Paolo V. // Physics Essays;Dec2007, Vol. 20 Issue 4, p629 

    Present-day computational mathematics tries to overcome the boundaries beset by time (of calculation) and space (of memory allocation). To this end, novel computational strategies have been developed in order to devise efficient numerical algorithms. One of these is based on the partial...

  • Development of an interactive molecular dynamics simulation software package. Knoll, P.; Mirzaei, S. // Review of Scientific Instruments;Apr2003, Vol. 74 Issue 4, p2483 

    Computer experiments play a significant role in science today. Molecular dynamic (MD) simulations are extremely powerful tools not only to understand and interpret the experiments at the microscopic level, but also to study regions that are not accessible experimentally. In the last few years...

  • A molecular dynamics study of freezing in a confined geometry. Ma, Wen-Jong; Banavar, Jayanth R.; Koplik, Joel // Journal of Chemical Physics;7/1/1992, Vol. 97 Issue 1, p485 

    The dynamics of freezing of a Lennard-Jones liquid in narrow channels bounded by molecular walls is studied by computer simulation. We quantify the time development of ordering and observe a novel freezing mechanism. The liquid forms layers and subsequent in-plane ordering within a layer is...

  • A structural analysis of the vitreous silica surface via a molecular dynamics computer simulation. Levine, S. M.; Garofalini, S. H. // Journal of Chemical Physics;3/1/1987, Vol. 86 Issue 5, p2997 

    Molecular dynamics computer simulations were used to study surfaces of pure silica glass. The potentials used here were those previously established to model bulk silica and have been extended to study surface relaxation in a perfect vacuum. A large number of surfaces were made using different...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics