DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. 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}
}

Journal Article:

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Mantid—Data analysis and visualization package for neutron scattering and μ 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
  • DOI: 10.1016/j.nima.2014.07.029

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
  • DOI: 10.1039/C4CP01164C

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
  • DOI: 10.1021/ar010034r

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
  • DOI: 10.1021/la901314b

Collective motions of hydrogen bonds
journal, November 1963


Pegasus, a workflow management system for science automation
journal, May 2015


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
  • DOI: 10.1002/jcc.20289

Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets
journal, July 2013


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
  • DOI: 10.1038/nmat779

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
  • DOI: 10.1021/jp981427j

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
  • DOI: 10.1021/acs.jctc.5b00878

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
  • DOI: 10.1021/mp400213z

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
  • DOI: 10.1021/jp807993f

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
  • DOI: 10.1177/1094342015594515

Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers
journal, July 2012


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
  • DOI: 10.1063/1.445869

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
  • DOI: 10.1021/ac00052a007

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
  • DOI: 10.1021/jz401406c

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
  • DOI: 10.1002/jcc.21287

Space-Time Correlation Function Formalism for Slow Neutron Scattering
journal, March 1960


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
  • DOI: 10.1021/ja00124a002

The properties and applications of nanodiamonds
journal, December 2011

  • Mochalin, Vadym N.; Shenderova, Olga; Ho, Dean
  • Nature Nanotechnology, Vol. 7, Issue 1
  • DOI: 10.1038/nnano.2011.209

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
  • DOI: 10.1038/ncomms4034

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
  • DOI: 10.1063/1.3626214

The emerging field of RNA nanotechnology
journal, November 2010


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
  • DOI: 10.1107/s1600576719012238

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
  • DOI: 10.1107/s1600576717016843