Sassena - X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers

Computer Physics Communications

Volumn 183, Issue 7, 2012, Pages 1491-1501

  Lindner, Benjamin ^a,b   Smith, Jeremy C ^a,b  

^a UNIVERSITY OF TENNESSEE   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Massively parallel; Molecular dynamics; Neutron; Scattering; X ray

Indexed keywords

BANDWIDTH REQUIREMENT; BENCHMARK SYSTEM; DATA STAGING; DEGREE OF PARALLELISM; HIGH PERFORMANCE COMPUTING; HIGH-PERFORMANCE TOOLS; LINEAR SCALING; MASSIVELY PARALLEL; MASSIVELY PARALLEL COMPUTERS; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR DYNAMICS TRAJECTORIES; OAK RIDGE NATIONAL LABORATORY; PARALLEL SUPERCOMPUTER; SCATTERING CALCULATIONS; SCATTERING INTENSITY; TIME-SCALES;

COMPUTER SIMULATION; COMPUTER SOFTWARE; NEUTRON SCATTERING; NEUTRONS; SCATTERING; SUPERCOMPUTERS; X RAYS;

MOLECULAR DYNAMICS;

EID: 84862822294     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2012.02.010     Document Type: Article

References (31)

1. O. Glatter The inverse scattering problem in small-angle scattering Neutrons, X-rays and Light. Scattering Methods Applied to Soft Condensed Matter 2002 Elsevier Science 73 103
2. Frank Noé, Sören Doose, Isabella Daidone, Marc Löllmann, Markus Sauer, John D. Chodera, and Jeremy C. Smith Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments PNAS 108 12 March 2011 4822 4827
3. Jeremy C. Smith, and G.R. Kneller Combination of neutron scattering and molecular dynamics to determine internal motions in biomolecules Molecular Simulation 10 2-6 1993 363 375
4. Franci Merzel, and Jeremy C. Smith SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins Acta Crystallographica Section D Biological Crystallography 58 2002 242 249 (Pubitemid 34179194)
5. F. Merzel, and Jeremy C. Smith Is the first hydration shell of lysozyme of higher density than bulk water? Proceedings of the National Academy of Sciences 99 8 April 2002 5378 5383 (Pubitemid 34411556)
6. P. Faure, A. Micu, D. Perahia, J. Doucet, Jeremy C. Smith, and J.P. Benoit Correlated intramolecular motions and diffuse X-ray scattering in lysozyme Nature Structural & Molecular Biology 1 2 February 1994 124 128 (Pubitemid 24974826)
7. A. Micu, and Jeremy C. Smith SERENA: a program for calculating X-ray diffuse scattering intensities from molecular dynamics trajectories Computer Physics Communications 91 1-3 September 1995 331 338
8. Lars Meinhold, and Jeremy C. Smith Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease Biophysical Journal 88 April 2005 2554 2563 (Pubitemid 40976124)
9. T. Róg, K. Murzyn, K. Hinsen, and G.R. Kneller nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations Journal of Computational Chemistry 24 5 April 2003 657 667
10. D. Svergun, and C. Barberato CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates Journal of Applied Crystallography 28 1995 768 773 (Pubitemid 3014671)
11. Roland Schulz, Benjamin Lindner, Loukas Petridis, and Jeremy C. Smith Scaling of multimillion-atom biological molecular dynamics simulation on a petascale supercomputer Journal of Chemical Theory and Computation 5 June 2009 2798 2808
12. Marc Bee Quasielastic Neutron Scattering: Principles and Applications in Solid State Chemistry, Biology and Material Science Dec. 1988 Adam Hilger
13. Th. Zemb, and P. Lindner Neutrons, X-rays and Light: Scattering Methods Applied to Soft Condensed Matter 2002 Elsevier Boston, Amsterdam
14. G.L. Squires Introduction to the Theory of Thermal Neutron Scattering 1996 Dover Publications New York 1978
15. J.M. Cowley, B.L.M. Peng, I.G. Ren, J.S.L. Dudarevc, M.J. Whelanc, Parameterizations of electron atomic scattering factors, International Tables for Crystallography, C (Ch. 4.3), 2006, p. 262.
16. Varley F. Sears Neutron scattering lengths and cross sections Neutron News 3 1992 26 37
17. B.O.O.S.T. Developers, Boost C++ Libraries, March 2011, http://www.boost.org.
18. Open MPI Developers, Open MPI, March 2011, http://www.open-mpi.org.
19. F.F.T.W. Developers, FFTW v3.2.2 Library, March 2011, http://www.fftw.org/.
20. G.R.O.M.A.C.S. Developers, Gromacs XDR File v1.1, March 2011, http://www.gromacs.org.
21. The HDF5 Group, HDF5, March 2011, http://www.hdfgroup.org/HDF5/.
22. LibXML developers, libxml, March 2011, http://xmlsoft.org/.
23. Daniel J. Cosgrove Growth of the plant cell wall Nature Reviews Molecular Cell Biology 6 11 November 2005 850 861 (Pubitemid 41568734)
24. Y. Nishiyama, P. Langan, and H. Chanzy Crystal structure and hydrogen-bonding system in cellulose 1 beta from synchrotron X-ray and neutron fiber diffraction Journal of the American Chemical Society 124 31 2002 9074 9082 (Pubitemid 34847668)
25. She-You Ding, and Michael E. Himmel The maize primary cell wall microfibril: a new model derived from direct visualization Journal of Agricultural and Food Chemistry 2006
26. Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl, GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation.
27. Michelle Kuttel, John W. Brady, and Kevin J. Naidoo Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations Journal of Computational Chemistry 23 13 2002 1236 1243 (Pubitemid 35017037)
28. Samira Elazzouzi-Hafraoui, Yoshiharu Nishiyama, Jean-Luc Putaux, Laurent Heux, Fredric Dubreuil, and Cyrille Rochas The shape and size distribution of crystalline nanoparticles prepared by acid hydrolysis of native cellulose Biomacromolecules 9 1 2008 57 65 (Pubitemid 351201582)
29. Imke Diddens, Bridget Murphy, Michael Krisch, and Martin Müller Anisotropic elastic properties of cellulose measured using inelastic X-ray scattering Macromolecules 41 November 2008 9755 9759
30. Siddhartha Chib, Siddhartha Chib, and Edward Greenberg Understanding the Metropolis-Hastings algorithm The American Statistician 49 4 November 1995 327 335 (Pubitemid 126008969)
31. M. Abramowitz, and I.A. Stegun Handbook of Mathematical Functions Mar. 1970 Dover New York