Workshop on Molecular Dynamics on Parallel Computers : John von Neumann Institute for Computing (NIC), Research Centre Julich, Germany, 8-10 February 1999 / edited by Rudiger Esser ... [et al.].

Format:

Book

Conference/Event

Author/Creator:

Workshop on Molecular Dynamics on Parallel Computers, Corporate Author.

Contributor:

Esser, Rüdiger.

Conference Name:

Workshop on Molecular Dynamics on Parallel Computers (1999 : John von Neumann Institute for Computing)

Language:

English

Subjects (All):

Molecular dynamics--Computer simulation--Congresses.

Molecular dynamics.

Parallel computers--Congresses.

Parallel computers.

Physical Description:

1 online resource (395 p.)

Place of Publication:

Singapore ; River Edge, NJ : World Scientific, c2000.

Language Note:

English

Summary:

Molecular dynamics is a well-established technique for simulating complex many-particle systems in many areas of physics, chemistry, and astrophysics. The huge computational requirements for simulations of large systems, especially with long-range forces, demand the use of massively parallel computers. Designing efficient algorithms for these problems is a highly non-trivial task.This book contains the invited talks and abstracts presented at a conference by more than 100 researchers from various fields: computer science, solid state physics, high energy physics, polymers, biochemistry, granul

Contents:

PREFACE; CONTENTS; INVITED PAPERS; Algorithms and Programs; ON THE NUMERICAL SIMULATION OF FULLERENE NANOTUBES: C100.000.000 AND BEYOND !; 1 Introduction; 2 Basic algorithm, time integration, implementation; 3 Potentials for Hydrocarbons; 3. 1 Brenner's potential; 3.2 Implementation of Brenner's potential; 3.3 The final algorithm; 4 Parallelization; 5 Numerical experiments; 5.1 Reactive collision of buckyballs with benzyne; 5.2 Nanotube simulations; 5.3 Parallelization results; 6 Concluding remarks; Acknowledgments; Appendix; References

ON DYNAMICAL TRANSITIONS BETWEEN CONFORMATIONAL ENSEMBLES1 Introduction; 2 Method; 2.1 Physical representation; 2.2 Spatial transition operator; 2.3 Discretization of the spatial transition operator; 2.4 Realization of the transition matrix via Hybrid Monte Carlo; 2.5 Conformational sampling via adaptive temperature Hybrid Monte Carlo; 3 Results and Discussion; 3. 1 ATHMC sampling; 3.2 Conformational analysis of the transition matrix; 3.3 Conclusion; References; MOLECULAR DYNAMICS ALGORITHMS FOR MASSIVELY PARALLEL COMPUTERS; 1 Introduction; 2 Motivation

3 Parallel Force Evaluation in Molecular Dynamics3.1 Neighbor Lists; 3.2 Particle Decomposition Method; 3.3 Spatial Decomposition Method; 4 Molecular Dynamics Program Design; 4.1 General Comments; 4.2 Program Design; 5 Software Engineering; 5.1 Interface to Communication Libraries; 5.2 Data Types and Function Overloading; 5.3 Preventing Local Array Copies; 5.4 Variables Related to Communication Libraries; 5.5 Programming Interface; 5.6 Module Dependencies; 6 Hardware Considerations; 7 Benchmarks; 7.1 Proper MD Programs for Comparison; 7.2 The Benchmark Run; 7.3 Further Benchmark Remarks

8 Concluding RemarksAcknowledgments; References; THE MOLECULAR DYNAMICS MODULE OF NWCHEM - DESIGN AND APPLICATION IN PROTEIN SIMULATIONS; 1 Introduction; 2 Domain Decomposition; 3 Communication; 4 Long-range Interactions; 5 Load-balancing; 6 Parallel Performance; 7 Practical Usage; Acknowledgments; References; IMD - A MOLECULAR DYNAMICS PROGRAM AND APPLICATIONS; 1 Introduction; 2 Basic Concepts of Short Range Massively-Parallel MD Simulations; 2.1 Cells on Parallel Computers; 3 Online Visualization and the Generation of Pictures; 3.1 Pictures; 4 Metacomputing; 4.1 Metacomputing with PACX

4.2 Special Requirements for Metacomputing5 Applications: Shock Waves in Quasicrystals and Crystals; 5.1 Shock Waves; Acknowledgments; References; Polymers; FROM MICROSCOPIC TO SEMI-MACROSCOPIC MODELING OF POLYMERS; 1 Introduction; 2 Systematic Coarse Graining Procedure; 3 Inverse Mapping from Mesoscopic back to Microscopic Regime; 4 An Even Coarser View on Polymers; 5 Conclusion; Acknowledgements; References; ADVANCED CBMC TECHNIQUES; 1 Introduction; 2 Dual cut-off CBMC; 3 Parallel CBMC; 4 Generation of trial segments; Concluding remarks; Acknowledgments; Appendix A: Details of the model

Appendix B: Details of the parallel computers used

Notes:

Description based upon print version of record.

Includes bibliographical references.

ISBN:

981-279-376-3