Parallel molecular dynamics

Hilbers P A J and Esselink K 1992 Parallel molecular dynamics Parallel Computing From Theory to Sound Praotloe ed W Joosen and E Mllgrom (Amsterdam lOS Press) pp 288-99... 

Berendsen, Van der Spoel, D. Van Drunen, R. GROMACS A message-passing parallel molecular dynamics implementation. Comput. Phys. Comm. 91 (1995) 43-56. 

NAMD [7] was born of frustration with the maintainability of previous locally developed parallel molecular dynamics codes. The primary goal of being able to hand the program down to the next generation of developers is reflected in the acronym NAMD Not (just) Another Molecular Dynamics code. Specific design requirements for NAMD were to run in parallel on the group s then recently purchased workstation cluster [8] and to use the fast multipole algorithm [9] for efficient full electrostatics evaluation as implemented in DPMTA [10]. 

Parallel molecular dynamics codes are distinguished by their methods of dividing the force evaluation workload among the processors (or nodes). The force evaluation is naturally divided into bonded terms, approximating the effects of covalent bonds and involving up to four nearby atoms, and pairwise nonbonded terms, which account for the electrostatic, dispersive, and electronic repulsion interactions between atoms that are not covalently bonded. The nonbonded forces involve interactions between all pairs of particles in the system and hence require time proportional to the square of the number of atoms. Even when neglected outside of a cutoff, nonbonded force evaluations represent the vast majority of work involved in a molecular dynamics simulation. 

Clark, T., Hanxleden, R., McCammon, J., Scott, L. Parallelizing molecular dynamics using spatial decomposition. In Proceedings of the scalable high performance computing conference. May 23-25, 1994, Knoxville, Tennessee. IEEE Computer Society Press, Los Alamitos, California, 1994. 

Parallel Molecular Dynamics Using Force Decomposition... 

T. W. Clark, J. A. McCammon, L. R. Scott, Parallel molecular dynamics , Proc. of the fifth SIAM conference on Parallel Processing for Scientific Computing, 338-44, 1992. 

Y. Hwang, R. Das, F. H. Saltz, M. Hadoscek and B. R. Brooks, Parallelizing molecular dynamics programs for distributed-memory machines , IEEE Computational Science and Engineering, Vol 2, no 2, 18-29, 1995. 

V. E. Taylor, R. L. Stevens and K. E. Arnold, Parallel molecular dynamics Communication requirements for massively parallel machines , Proc. Frontiers... 

Kald, L. Skeel, R. Bhandarkar, M. Brunner, R. Gursoy, A. Krawetz, N. Phillips, J. Shinozaki, A. Varadarajan, K. Schulten, K., NAMD2 Greater scalability for parallel molecular dynamics, J. Comput. Phys. 1999,151, 283-312... 

Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, et al. 1999. NAMD2 greater scalability for parallel molecular dynamics. Comput Phys 151 283-312. 

R. Das and J. Saltz, in Parallel Processing for Scientific Computing, Sixth SIAM Conference, Norfolk, VA, March 22-24, 1993, R. F. Sincovec, D. E. Keyes, M. R. Leuze, L. R. Petzold, and D. A. Reed, Eds., Society for Industrial and Applied Mathematics, Philadelphia, 1993, pp. 187-192. Parallelizing Molecular Dynamics Codes Using PARTI Software Primitives. 

S. J. Plimpton, in Proceedings of the Scalable High Performance Computing Conference SHPCC-92, Williamsburg, VA, April 26-29 1992, IEEE Computer Society Press, Los Alamitos, CA, 1992, pp. 246-251. Scalable Parallel Molecular Dynamics on MIMD Supercomputers. 

S. J. Plimpton and B. A. Hendrickson, Mater. Theory Modeling, 291, 37 (1992). Parallel Molecular Dynamics with the Embedded Atom Method. 

Chapter 7. Large scale parallel molecular dynamics simulations Fredrik Hedman and Aatto Laaksonen... 

Large Scale Parallel Molecular Dynamics Simulations... 

F. Hedman and A. Laaksonen, A Data-parallel Molecular Dynamics Method for Liquids with Coulombic Interactions, Mol. Simul., 14 (1995), 235-244. 

S. Plimpton and B. Hendrickson, Parallel Molecular Dynamics Algorithms for Simulation of Molecular Systems, in Mattson [110], 114-132. 

M. Surridge, D. J. Tildesley, Y. C. Kong, and D. B. Adolf, A parallel molecular dynamics simulation code for dialkyl cationic surfactants. Parallel Comput., 22 (1996), 1053-1071. 

Gomes, C.J., M. Madrid, and C.H. Amon. Parallel Molecular Dynamics Code Validation Through Bulk Silicon Thermal Conductivity Calculations, in Proceedings of the 2003 ASME International Mechanical Engineering Congress and Exposition, IMECE 2003-42352. 2003. Washington, DC. Lee, Y.H., R. Biswas, C.M. Soukoulis, C.Z. Wang, C.T. Chan, and K.M. Ho, Molecular-Dynamics Simulation of Thermal Conductivity in Amorphous Silicon. Physical Review B, 1991.43(8) p. 6573-6580. 

W. Smith and T. R. Forester, J. Mol. Graphics, 14, 136 (1996). DL Poly 2.0—A General Purpose Parallel Molecular Dynamics Simulation Package. 

Kodiyalam S, Kalia RK, Kikuchi H, Nakano A, Shimojo F, Vashishta P (2001) Grain boundaries in gallium arsenide nanocrystals underpressure A parallel molecular-dynamics study. Phys Rev Letters 86 55-58 Leoni S, Nesper R (2000) Elucidation of simple pathways for reconstractive phase transitions using periodic equi-surface (PES) descriptors. The silica phase system. 1. Quartz-tridymite. Acta Crystallogr A 56 383-393... 

Kalia RK, Campbell TJ, Chatteqee A, Nakano A, Vashishta P, Ogata S (2000) Multiresolution algorithms for massively parallel molecular dynamics simulations of nanostructured materials. Computer Phys Commun 128 245-259... 

The extended simple point charge (SPC/E) model [59] is used. This model is known to give reasonably accurate values of static dielectric permittivity of liquid water at ambient conditions [60]. The MD simulations were performed for both H2O and D2O with the system size of 1024 particles at 220 K, 240 K, 267 K, 273 K, 300 K, and 355 K. The parallel molecular dynamics code for arbitrary molecular mixtures (DynaMix) is implemented by Lyubartsev and Laaksonen [61]. The simulations have been carried out on a Linux cluster built on the Tyan/Opteron 64 platform, which enables calculations of relatively long trajectories for a system of 1024 water molecules. The simulation run lengths depend on temperature and are in the range between 1 ns and 4 ns for the warmest and coldest simulation, respectively. As the initial condition was a cubic lattice, the equilibration time was chosen to be temperature dependent in the range from 200 ps at 355 Ktol ns at 200K. 

DL POLY. DL POLY is a parallel molecular dynamics simulation package originally developed at the Daresbury Laboratory in England. Parameters for the current DL POLY 3 force field may be obtained from the GRO-MOS, AMBER, and DREIDING force fields that share functional forms. 

LAMMPS. Another message-passing MD code is LAMMPS [33] used for high-performance parallelized molecular dynamics calculations. The current version (version 17) is compatible with both AMBER and CHARMM. 

M. R. Wilson, Parallel molecular dynamics techniques for the simulation of anisotropic systems. In P. Pasini, and C. Zannoni editors. Advances in computer simulation of liquid crystals, volume 545 of Series C Mathematical and Physical Sciences, chapter 13. Kluwer Academic Publishers, 2000. 

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