W. F. van Gunsteren, H. J. C. Berendsen, F. Colonna, D. Perahia, J. P. Hollenberg, and D. Lellouch. On searching neighbors in computer simulations of macromolecular systems. Journal of Computational Chemistry, 5(3):272--279, 1984. Home/Search Document Not in Database Summary Related Articles Check |
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Parallel GROMOS Users Guide - University Of (Correct)
.... and nonbonded force calculation 4 5 Load balancing the nonbonded force calculation 4 6 Timing 8 7 Standard input 9 8 File I O 10 9 Making and running 1 INTRODUCTION 2 1 Introduction GROMOS (GROningen MOlecular Simulation) is a suite of programs designed for the dynamic modeling of biomolecules [5, 7]. GROMOS provides programs for the simulation of biological molecules (and arbitrary molecules) using molecular dynamics or stochastic dynamics. In addition, energy minimization and analysis programs are provided. The molecular dynamics program, GROMOS, has been parallelized for the distributed ....
W. F. van Gunsteren, H. J. C. Berendsen, F. Colonna, D. Perahia, J. P. Hollenberg, and D. Lellouch. On searching neighbors in computer simulations of macromolecular systems. Journal of Computational Chemistry, 5(3):272--279, 1984.
Parallelization Strategies for a Molecular Dynamics.. - Clark, Hanxleden.. (1992) (11 citations) (Correct)
....c . Details of these phases are discussed in this section. Figure 1: Flowchart for UHGROMOS. The communication phases are shaded. Order of magnitude work estimates are given for P processors and N atoms. 3. 1 Pairlist distribution The GROMOS pairlist is represented as a pair of arrays, INB and JNB [4, 31]. For each atom I, INB(I) is the number of neighboring atoms residing within the cutoff radius of I. Returning to the notation introduced in Section 2.1, the UHGROMOS distribution of (I; J) results in a situation where the use of (I; J) can potentially access any or all of X and F . This is a ....
W. F. van Gunsteren, H. J. C. Berendsen, F. Colonna, D. Perahia, J. P. Hollenberg, and D. Lellouch. On searching neighbors in computer simulations of macromolecular systems. Journal of Computational Chemistry, 5(3):272-- 279, 1984.
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