Enhanced molecular dynamics performance with a programmable graphics processor

Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware necessitates a reformulation of the underlying algorithm. Performance measurements demonstrate the considerable benefit and cost-effectiveness of such an approach, which produces a factor of 2.5 speed improvement over previous work for the case of the soft-sphere potential.Comment: 20 pages (v2: minor additions and changes; v3: corrected typos

Modeling growth of 60-unit shells in solution: Early results

AbstractCurrent research into supramolecular assembly using molecular dynamics simulation is summarized. Ongoing simulations are aimed at exploring the nature of the growth pathways of larger shells than considered previously, under reversible bonding conditions and in the presence of an explicit solvent

Dynamics of polymer chain collapse into compact states

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional interactions. Different native-state packing arrangements and chain lengths are explored; the organization of the native state is found to affect both the ability of the chain to fold successfully and the nature of the folding pathway as the system is gradually cooled. An order parameter based on contact counts is used to provide information about the folding process, with contacts additionally classified according to criteria such as core and surface sites or local and distant site pairs. Fully detailed contact maps and their evolution are also examined.Comment: 11 pages, 11 figures (some low resolution

Star-graph expansions for bond-diluted Potts models

We derive high-temperature series expansions for the free energy and the susceptibility of random-bond $q$-state Potts models on hypercubic lattices using a star-graph expansion technique. This method enables the exact calculation of quenched disorder averages for arbitrary uncorrelated coupling distributions. Moreover, we can keep the disorder strength $p$ as well as the dimension $d$ as symbolic parameters. By applying several series analysis techniques to the new series expansions, one can scan large regions of the $(p,d)$ parameter space for any value of $q$. For the bond-diluted 4-state Potts model in three dimensions, which exhibits a rather strong first-order phase transition in the undiluted case, we present results for the transition temperature and the effective critical exponent $\gamma$ as a function of $p$ as obtained from the analysis of susceptibility series up to order 18. A comparison with recent Monte Carlo data (Chatelain {\em et al.}, Phys. Rev. E64, 036120(2001)) shows signals for the softening to a second-order transition at finite disorder strength.Comment: 8 pages, 6 figure

Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces

A new algorithm for calculating intermolecular pair forces in molecular dynamics (MD) simulations on a distributed parallel computer is presented. The arbitrary interacting cells algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh that has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid mechanics simulation by MD in complex geometries, and to provide the MD component of a hybrid MD/continuum simulation. The spatial relationship of the cells of the mesh is calculated at the start of the simulation and only the molecules contained in cells that have part of their surface closer than the cut-off radius of the intermolecular pair potential are required to interact. AICA has been implemented in the open source C++ code OpenFOAM, and its accuracy has been indirectly verified against a published MD code. The same system simulated in serial and in parallel on 12 and 32 processors gives the same results. Performance tests show that there is an optimal number of cells in a mesh for maximum speed of calculating intermolecular forces, and that having a large number of empty cells in the mesh does not add a significant computational overhead

Algorithm for numerical integration of the rigid-body equations of motion

A new algorithm for numerical integration of the rigid-body equations of motion is proposed. The algorithm uses the leapfrog scheme and the quantities involved are angular velocities and orientational variables which can be expressed in terms of either principal axes or quaternions. Due to specific features of the algorithm, orthonormality and unit norms of the orientational variables are integrals of motion, despite an approximate character of the produced trajectories. It is shown that the method presented appears to be the most efficient among all known algorithms of such a kind.Comment: 4 pages, 1 figur

Spin dynamics simulations of the magnetic dynamics of RbMnF3_3 and direct comparison with experiment

Spin-dynamics techniques have been used to perform large-scale simulations of the dynamic behavior of the classical Heisenberg antiferromagnet in simple cubic lattices with linear sizes $L\leq 60$. This system is widely recognized as an appropriate model for the magnetic properties of RbMnF$_3$. Time-evolutions of spin configurations were determined numerically from coupled equations of motion for individual spins using a new algorithm implemented by Krech {\it etal}, which is based on fourth-order Suzuki-Trotter decompositions of exponential operators. The dynamic structure factor was calculated from the space- and time-displaced spin-spin correlation function. The crossover from hydrodynamic to critical behavior of the dispersion curve and spin-wave half-width was studied as the temperature was increased towards the critical temperature. The dynamic critical exponent was estimated to be $z=(1.43\pm 0.03)$, which is slightly lower than the dynamic scaling prediction, but in good agreement with a recent experimental value. Direct, quantitative comparisons of both the dispersion curve and the lineshapes obtained from our simulations with very recent experimental results for RbMnF$_3$ are presented.Comment: 30 pages, RevTex, 9 figures, to appear in PR

Self-avoiding walks and connective constants in small-world networks

Long-distance characteristics of small-world networks have been studied by means of self-avoiding walks (SAW's). We consider networks generated by rewiring links in one- and two-dimensional regular lattices. The number of SAW's $u_n$ was obtained from numerical simulations as a function of the number of steps $n$ on the considered networks. The so-called connective constant, $\mu = \lim_{n \to \infty} u_n/u_{n-1}$, which characterizes the long-distance behavior of the walks, increases continuously with disorder strength (or rewiring probability, $p$). For small $p$, one has a linear relation $\mu = \mu_0 + a p$, $\mu_0$ and $a$ being constants dependent on the underlying lattice. Close to $p = 1$ one finds the behavior expected for random graphs. An analytical approach is given to account for the results derived from numerical simulations. Both methods yield results agreeing with each other for small $p$, and differ for $p$ close to 1, because of the different connectivity distributions resulting in both cases.Comment: 7 pages, 5 figure