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

Lynch, Vickie E.; Borreguero, Jose M.; Bhowmik, Debsindhu; Ganesh, Panchapakesan; Sumpter, Bobby G.; Proffen, Thomas E.; 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:1376601

^[1];

^[1]; Ganesh, Panchapakesan ^[1]; Sumpter, Bobby G. ^[1];

^[1]; Goswami, Monojoy ^[1]

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

Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. In order to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. Here, we describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D₂O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. In order to compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.

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Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)

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

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

OSTI ID:: 1376601

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

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

References (26)

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
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
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
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
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
Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study Dhindsa, Gurpreet K.; Bhowmik, Debsindhu; Goswami, Monojoy The Journal of Physical Chemistry B, Vol. 120, Issue 38 https://doi.org/10.1021/acs.jpcb.6b07511	journal	September 2016
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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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
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

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