An automated analysis workflow for optimization of force-field parameters using neutron scattering data

Lynch, Vickie E.; Borreguero Calvo, Jose M.; Bhowmik, Debsindhu; Ganesh, Panchapakesan; Sumpter, Bobby; Proffen, Thomas; Goswami, Monojoy

doi:10.1016/j.jcp.2017.03.045

Title: An automated analysis workflow for optimization of force-field parameters using neutron scattering data

Journal Article · Mon Mar 27 00:00:00 EDT 2017 · Journal of Computational Physics

DOI:https://doi.org/10.1016/j.jcp.2017.03.045· OSTI ID:1769253

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Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

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Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231; SC0012636

OSTI ID:: 1769253

Alternate ID(s):: OSTI ID: 1396729

Journal Information:: Journal of Computational Physics, Vol. 340; ISSN 0021-9991

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 6 works

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References (25)

Mantid—Data analysis and visualization package for neutron scattering and $μ$ SR experiments Arnold, O.; Bilheux, J. C.; Borreguero, J. M. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 764 https://doi.org/10.1016/j.nima.2014.07.029	journal	November 2014
Aqueous solutions of tetraalkylammonium halides: ion hydration, dynamics and ion–ion interactions in light of steric effects Bhowmik, Debsindhu; Malikova, Natalie; Mériguet, Guillaume Phys. Chem. Chem. Phys., Vol. 16, Issue 26 https://doi.org/10.1039/C4CP01164C	journal	January 2014
Molecular Dynamics Applied to X-ray Structure Refinement Brunger, Axel T.; Adams, Paul D. Accounts of Chemical Research, Vol. 35, Issue 6 https://doi.org/10.1021/ar010034r	journal	June 2002
Interfacial Water at Hydrophobic and Hydrophilic Surfaces: Slip, Viscosity, and Diffusion Sendner, Christian; Horinek, Dominik; Bocquet, Lyderic Langmuir, Vol. 25, Issue 18 https://doi.org/10.1021/la901314b	journal	September 2009
Collective motions of hydrogen bonds de Gennes, P. G. Solid State Communications, Vol. 1, Issue 6 https://doi.org/10.1016/0038-1098(63)90212-6	journal	November 1963
Pegasus, a workflow management system for science automation Deelman, Ewa; Vahi, Karan; Juve, Gideon Future Generation Computer Systems, Vol. 46 https://doi.org/10.1016/j.future.2014.10.008	journal	May 2015
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets Tu, Yusong; Lv, Min; Xiu, Peng Nature Nanotechnology, Vol. 8, Issue 8 https://doi.org/10.1038/nnano.2013.125	journal	July 2013
DNA-modified nanocrystalline diamond thin-films as stable, biologically active substrates Yang, Wensha; Auciello, Orlando; Butler, James E. Nature Materials, Vol. 1, Issue 4 https://doi.org/10.1038/nmat779	journal	November 2002
Hydration and Dynamics of a Tetramethylammonium Ion in Water: A Computer Simulation Study García-Tarrés, L.; Guàrdia, E. The Journal of Physical Chemistry B, Vol. 102, Issue 38 https://doi.org/10.1021/jp981427j	journal	September 1998
Molecular Dynamics Force-Field Refinement against Quasi-Elastic Neutron Scattering Data Borreguero, Jose M.; Lynch, Vickie E. Journal of Chemical Theory and Computation, Vol. 12, Issue 1 https://doi.org/10.1021/acs.jctc.5b00878	journal	December 2015
Adsorption of Drugs on Nanodiamond: Toward Development of a Drug Delivery Platform Mochalin, Vadym N.; Pentecost, Amanda; Li, Xue-Mei Molecular Pharmaceutics, Vol. 10, Issue 10 https://doi.org/10.1021/mp400213z	journal	August 2013
Ion-Specific Interactions between Halides and Basic Amino Acids in Water ^† Heyda, Jan; Hrobárik, Tomáš; Jungwirth, Pavel The Journal of Physical Chemistry A, Vol. 113, Issue 10 https://doi.org/10.1021/jp807993f	journal	March 2009
PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows Deelman, Ewa; Carothers, Christopher; Mandal, Anirban The International Journal of High Performance Computing Applications, Vol. 31, Issue 1 https://doi.org/10.1177/1094342015594515	journal	July 2016
Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers Lindner, Benjamin; Smith, Jeremy C. Computer Physics Communications, Vol. 183, Issue 7 https://doi.org/10.1016/j.cpc.2012.02.010	journal	July 2012
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
The electrochemical activity of boron-doped polycrystalline diamond thin film electrodes Swain, Greg M.; Ramesham, Rajeshuni. Analytical Chemistry, Vol. 65, Issue 4 https://doi.org/10.1021/ac00052a007	journal	February 1993
Role of Water and Ions on the Dynamical Transition of RNA Zhang, Hailiang; Khodadadi, Sheila; Fiedler, Steven L. The Journal of Physical Chemistry Letters, Vol. 4, Issue 19 https://doi.org/10.1021/jz401406c	journal	September 2013
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
Space-Time Correlation Function Formalism for Slow Neutron Scattering Schofield, P. Physical Review Letters, Vol. 4, Issue 5 https://doi.org/10.1103/PhysRevLett.4.239	journal	March 1960
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I. Journal of the American Chemical Society, Vol. 117, Issue 19 https://doi.org/10.1021/ja00124a002	journal	May 1995
The properties and applications of nanodiamonds Mochalin, Vadym N.; Shenderova, Olga; Ho, Dean Nature Nanotechnology, Vol. 7, Issue 1 https://doi.org/10.1038/nnano.2011.209	journal	December 2011
Dynamic heterogeneity controls diffusion and viscosity near biological interfaces Pronk, Sander; Lindahl, Erik; Kasson, Peter M. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4034	journal	January 2014
A time-of-flight backscattering spectrometer at the Spallation Neutron Source, BASIS Mamontov, E.; Herwig, K. W. Review of Scientific Instruments, Vol. 82, Issue 8 https://doi.org/10.1063/1.3626214	journal	August 2011
The emerging field of RNA nanotechnology Guo, Peixuan Nature Nanotechnology, Vol. 5, Issue 12 https://doi.org/10.1038/nnano.2010.231	journal	November 2010

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Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment Gavezzotti, Angelo; Lo Presti, Leonardo Journal of Applied Crystallography, Vol. 52, Issue 6 https://doi.org/10.1107/s1600576719012238	journal	October 2019
Evaluation of nano- and mesoscale structural features in composite materials through hierarchical decomposition of the radial distribution function García-Negrón, Valerie; Oyedele, Akinola D.; Ponce, Eduardo Journal of Applied Crystallography, Vol. 51, Issue 1 https://doi.org/10.1107/s1600576717016843	journal	February 2018

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97 MATHEMATICS AND COMPUTING
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Title: An automated analysis workflow for optimization of force-field parameters using neutron scattering data

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