Paper Citing NAMD - Abstract
Reith, Daniel; Mirny, Leonid; Virnau, Peter
GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling
PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT, Issue 191, 135-145, 2011
We report on equilibrium properties of a concentrated solution of non-concatenated ring polymers by Molecular dynamics simulations using HooMD-blue, a fast implementation on graphics processor units (CPUs). We are able to identify the intermediate scaling regime for the radius of gyration R-g proportional to N-0.4 as well as indication for a crossover to R-g proportional to N-1/3 for rings with chain length N in our fully flexible off-lattice polymer model. This crossover takes place between a ring size of 2500 and 7500 monomers for monomer density rho = 0.5. Our results are in agreement with recent studies for lattice and stiff off-lattice models and show once again that this scaling is not model dependent at all. Furthermore this study demonstrates that CPUs are suited to tackle large scale problems in computational polymer science. To this end we present performance measurements relating the computing performance of a single NVidias GTX580 consumer graphic card to conventional state of the art supercomputers.
