An automated analysis workflow for optimization of force-field parameters using neutron scattering data
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1769253
- Alternate Identifier(s):
- OSTI ID: 1396729
- Grant/Contract Number:
- AC05-00OR22725; AC02-05CH11231; SC0012636
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Computational Physics
- Additional Journal Information:
- Journal Volume: 340; Journal ID: ISSN 0021-9991
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; Force-field optimization; Molecular dynamics; Neutron data analysis; Quasi-elastic neutron scattering; Biopolymers; CHARMM
Citation Formats
Lynch, Vickie E., Borreguero Calvo, Jose M., Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby, Proffen, Thomas, and Goswami, Monojoy. An automated analysis workflow for optimization of force-field parameters using neutron scattering data. United States: N. p., 2017.
Web. doi:10.1016/j.jcp.2017.03.045.
Lynch, Vickie E., Borreguero Calvo, Jose M., Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby, Proffen, Thomas, & Goswami, Monojoy. An automated analysis workflow for optimization of force-field parameters using neutron scattering data. United States. https://doi.org/10.1016/j.jcp.2017.03.045
Lynch, Vickie E., Borreguero Calvo, Jose M., Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby, Proffen, Thomas, and Goswami, Monojoy. Mon .
"An automated analysis workflow for optimization of force-field parameters using neutron scattering data". United States. https://doi.org/10.1016/j.jcp.2017.03.045. https://www.osti.gov/servlets/purl/1769253.
@article{osti_1769253,
title = {An automated analysis workflow for optimization of force-field parameters using neutron scattering data},
author = {Lynch, Vickie E. and Borreguero Calvo, Jose M. and Bhowmik, Debsindhu and Ganesh, Panchapakesan and Sumpter, Bobby and Proffen, Thomas and Goswami, Monojoy},
abstractNote = {},
doi = {10.1016/j.jcp.2017.03.045},
journal = {Journal of Computational Physics},
number = ,
volume = 340,
place = {United States},
year = {Mon Mar 27 00:00:00 EDT 2017},
month = {Mon Mar 27 00:00:00 EDT 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Cited by: 6 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Mantid—Data analysis and visualization package for neutron scattering and SR experiments
journal, November 2014
- 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
Aqueous solutions of tetraalkylammonium halides: ion hydration, dynamics and ion–ion interactions in light of steric effects
journal, January 2014
- Bhowmik, Debsindhu; Malikova, Natalie; Mériguet, Guillaume
- Phys. Chem. Chem. Phys., Vol. 16, Issue 26
Molecular Dynamics Applied to X-ray Structure Refinement
journal, June 2002
- Brunger, Axel T.; Adams, Paul D.
- Accounts of Chemical Research, Vol. 35, Issue 6
Interfacial Water at Hydrophobic and Hydrophilic Surfaces: Slip, Viscosity, and Diffusion
journal, September 2009
- Sendner, Christian; Horinek, Dominik; Bocquet, Lyderic
- Langmuir, Vol. 25, Issue 18
Collective motions of hydrogen bonds
journal, November 1963
- de Gennes, P. G.
- Solid State Communications, Vol. 1, Issue 6
Pegasus, a workflow management system for science automation
journal, May 2015
- Deelman, Ewa; Vahi, Karan; Juve, Gideon
- Future Generation Computer Systems, Vol. 46
Scalable molecular dynamics with NAMD
journal, January 2005
- Phillips, James C.; Braun, Rosemary; Wang, Wei
- Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets
journal, July 2013
- Tu, Yusong; Lv, Min; Xiu, Peng
- Nature Nanotechnology, Vol. 8, Issue 8
DNA-modified nanocrystalline diamond thin-films as stable, biologically active substrates
journal, November 2002
- Yang, Wensha; Auciello, Orlando; Butler, James E.
- Nature Materials, Vol. 1, Issue 4
Hydration and Dynamics of a Tetramethylammonium Ion in Water: A Computer Simulation Study
journal, September 1998
- García-Tarrés, L.; Guàrdia, E.
- The Journal of Physical Chemistry B, Vol. 102, Issue 38
Molecular Dynamics Force-Field Refinement against Quasi-Elastic Neutron Scattering Data
journal, December 2015
- Borreguero, Jose M.; Lynch, Vickie E.
- Journal of Chemical Theory and Computation, Vol. 12, Issue 1
Adsorption of Drugs on Nanodiamond: Toward Development of a Drug Delivery Platform
journal, August 2013
- Mochalin, Vadym N.; Pentecost, Amanda; Li, Xue-Mei
- Molecular Pharmaceutics, Vol. 10, Issue 10
Ion-Specific Interactions between Halides and Basic Amino Acids in Water †
journal, March 2009
- Heyda, Jan; Hrobárik, Tomáš; Jungwirth, Pavel
- The Journal of Physical Chemistry A, Vol. 113, Issue 10
PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows
journal, July 2016
- Deelman, Ewa; Carothers, Christopher; Mandal, Anirban
- The International Journal of High Performance Computing Applications, Vol. 31, Issue 1
Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers
journal, July 2012
- Lindner, Benjamin; Smith, Jeremy C.
- Computer Physics Communications, Vol. 183, Issue 7
Comparison of simple potential functions for simulating liquid water
journal, July 1983
- Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
- The Journal of Chemical Physics, Vol. 79, Issue 2
The electrochemical activity of boron-doped polycrystalline diamond thin film electrodes
journal, February 1993
- Swain, Greg M.; Ramesham, Rajeshuni.
- Analytical Chemistry, Vol. 65, Issue 4
Role of Water and Ions on the Dynamical Transition of RNA
journal, September 2013
- Zhang, Hailiang; Khodadadi, Sheila; Fiedler, Steven L.
- The Journal of Physical Chemistry Letters, Vol. 4, Issue 19
CHARMM: The biomolecular simulation program
journal, July 2009
- Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
- Journal of Computational Chemistry, Vol. 30, Issue 10
Space-Time Correlation Function Formalism for Slow Neutron Scattering
journal, March 1960
- Schofield, P.
- Physical Review Letters, Vol. 4, Issue 5
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
journal, May 1995
- Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.
- Journal of the American Chemical Society, Vol. 117, Issue 19
The properties and applications of nanodiamonds
journal, December 2011
- Mochalin, Vadym N.; Shenderova, Olga; Ho, Dean
- Nature Nanotechnology, Vol. 7, Issue 1
Dynamic heterogeneity controls diffusion and viscosity near biological interfaces
journal, January 2014
- Pronk, Sander; Lindahl, Erik; Kasson, Peter M.
- Nature Communications, Vol. 5, Issue 1
A time-of-flight backscattering spectrometer at the Spallation Neutron Source, BASIS
journal, August 2011
- Mamontov, E.; Herwig, K. W.
- Review of Scientific Instruments, Vol. 82, Issue 8
The emerging field of RNA nanotechnology
journal, November 2010
- Guo, Peixuan
- Nature Nanotechnology, Vol. 5, Issue 12
Works referencing / citing this record:
Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment
journal, October 2019
- Gavezzotti, Angelo; Lo Presti, Leonardo
- Journal of Applied Crystallography, Vol. 52, Issue 6
Evaluation of nano- and mesoscale structural features in composite materials through hierarchical decomposition of the radial distribution function
journal, February 2018
- García-Negrón, Valerie; Oyedele, Akinola D.; Ponce, Eduardo
- Journal of Applied Crystallography, Vol. 51, Issue 1