100
Views
5
CrossRef citations to date
0
Altmetric
Proceedings of the 3rd International Conference on Molecular Simulation

An efficiently extendable and fine-grain parallelised molecular dynamics simulation program: Mid

&
Pages 801-807 | Received 30 Jan 2014, Accepted 07 May 2014, Published online: 03 Jul 2014

References

  • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 1983;4:187–217.
  • Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem. 2005;26:1668–1688.
  • Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–1802.
  • Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4:435–447.
  • Bowers K, Chow E, Xu H, Dror R, Eastwood M, Gregersen B, Klepeis J, Kolossvary I, Moraes M, Sacerdoti F, Salmon J, Shan Y, Shaw D. Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the SC06 (High Performance Computing, Networking, Storage and Analysis), Tampa, FL, USA 2006 p. 43.
  • Andoh Y, Yoshii N, Fujimoto K, Mizutani K, Kojima H, Yamada A, Okazaki S, Kawaguchi K, Nagao H, Iwahashi K, Mizutani F, Minami K, Ichikawa S-i, Komatsu H, Ishizuki S, Takeda Y, Fukushima M. MODYLAS: a highly parallelized general-purpose molecular dynamics simulation program for large-scale systems with long-range forces calculated by fast multipole method (FMM) and highly scalable fine-grained new parallel processing algorithms. J Chem Theory Comput. 2013;9:3201–3209.
  • Yonezawa A, Watanabe T, Yokokawa M, Sato M, Hirao K. Advanced Institute for Computational Science (AICS): Japanese national high-performance computing research institute and its 10-petaflops supercomputer “K”. Proceedings of the SC11 (High Performance Computing, Networking, Storage and Analysis), Seattle, WA, USA 2011. p. 13:1–13:8.
  • Alexandrescu A. Modern C++ design: generic programming and design patterns applied. Chapter 1. Boston (MA): Addison-Wesley; 2001.
  • Miller TF III, Eleftheriou M, Pattnaik P, Ndirango A, Newns D, Martyna J. Symplectic quaternion scheme for biophysical molecular dynamics. J Chem Phys. 2002;116:8649–8659.
  • Nosé S. An improved symplectic integrator for Nosé–Poincaré thermostat. J Phys Soc Jpn. 2001;70:75–77.
  • Andersen HC. Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys. 1980;72:2384–2393.
  • Okumura H, Itoh SG, Okamotoc Y. Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles. J Chem Phys. 2007;126:1–17, 084103.
  • Tuckerman M, Berne BJ, Martyna GJ. Reversible multiple time scale molecular dynamics. J Chem Phys. 1992;97:1990–2001.
  • Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys. 1995;103:8577–8593.
  • Frigo M, Johnson SG. The design and implementation of FFTW3. Proc IEEE. 2005;93:216–231. Special issue on “Program Generation, Optimization, and Platform Adaptation”.
  • Snir M. A note on N-body computations with cutoffs. Theory Comput Syst. 2004;37:295–318.
  • Shaw DE. A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J Comput Chem. 2005;26:1318–1328.
  • Bowers KJ, Dror RO, Shaw DE. The midpoint method for parallelization of particle simulations. J Chem Phys. 2006;124:1–11, 184109.
  • Bowers KJ, Dror RO, Shaw E. Zonal methods for the parallel execution of range-limited N-body simulations. J Comput Phys. 2007;221:303–329.
  • Fitch BG, Rayshubskiy A, Eleftheriou M, Ward TJC, Giampapa M, Pitman MC, Germain R. Blue matter: approaching the limits of concurrency for classical molecular dynamics. Proceedings of the SC06 (High Performance Computing, Networking, Storage and Analysis), Tampa, FL, USA 2006. p. 44.
  • Tang PTP, Park J, Kim D, Petrov V. A Framework for Low-communication 1-D FFT. Proceedings of the SC12 (High Performance Computing, Networking, Storage and Analysis). Salt Lake City, UT, USA 2012. p. 42:1–42:12.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.