S. Gupta. Computing aspects of molecular dynamics simulations. Comp. Phys. Comm., 70:243--270, 1992. Home/Search Document Not in Database Summary Related Articles Check |
This paper is cited in the following contexts:
Parallel Molecular Dynamics Algorithms for Simulation of.. - Plimpton, Hendrickson (1995) (Correct)
....interactions with near neighbors. Parallelizing that portion of the computation is essentially the equivalent of the short range force calculations we will discuss here. Several techniques have been developed by various researchers for parallelizing short range MD simulations effectively [11, 15, 20, 24]. The purpose of this paper is to describe the different methods and highlight their respective advantages and disadvantages when applied to molecules, be they small molecule or macromolecular systems. We begin in the next section with a brief description of the computations that are performed in ....
S. Gupta. Computing aspects of molecular dynamics simulations. Comp. Phys. Comm., 70:243--270, 1992.
Fast Parallel Algorithms for Short-Range Molecular Dynamics - Plimpton (1995) (50 citations) (Correct)
....this parallelism. The goal in each is to divide the force computations in equation (1) evenly across the processors so as to extract maximum parallelism. To our knowledge, all algorithms that have been proposed or implemented (including ours) have been variations on these two methods. References [21, 25, 49] include good overviews of various techniques. In the first class of methods a pre determined set of force computations is assigned to each processor. The assignment remains fixed for the duration of the simulation. The simplest way of doing this is to give a subgroup of atoms to each processor. ....
....neighbor lists) on SIMD machines. Thus the scaling of these algorithms is different from the algorithm presented in Section 4 as is the way they distribute the atom data among processors and perform inter processor communication. 6 Spatial decomposition methods, also called geometric methods [21, 25], are more common in the literature because they are well suited to very large MD simulations. Recent parallel message passing implementations for the Intel iPSC 2 hypercube [39, 46, 49] CM 5 [9, 51] Fujitsu AP1000 [14] and a T800 Transputer machine [20] have some features in common with ....
S. Gupta. Computing aspects of molecular dynamics simulations. Comp. Phys. Comm., 70:243--270, 1992.
Distributed 2-D Molecular Dynamics Simulation on.. - Bubak, Moscinski, Pogoda (1996) (Correct)
....simulation are presented in the fifth section. Finally, the sixth section concludes the paper with an outlook on going on and future activities. 2 Calculation of forces The calculation of forces is always the most time consuming part of any MD program. We have applied the Verlet neighbor list [10] to speed up the evaluation of interactions between molecules and Hockney linked list is applied to build the neighbor list. Decision how often to reconstruct the neighbor list is taken automatically. Equations of motion are solved using leap frog algorithm. Tuning of the sequential program ....
Gupta, S. "Computing aspects of molecular dynamics simulation", Computer Physics Communication 70 (1992) 243-270.
Parallel Molecular Dynamics: Communication Requirements.. - Taylor, Stevens, Arnold (Correct)
No context found.
Gupta, S., "Computing Aspects of Molecular Dynamics Simulations," Physics Communications, 70:243-270, 1992.
Online articles have much greater impact More about CiteSeer.IST Add search form to your site Submit documents Feedback
CiteSeer.IST - Copyright Penn State and NEC