skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

Journal Article · · Journal of Chemical Physics
DOI:https://doi.org/10.1063/1.4947253· OSTI ID:1260415
 [1];  [1];  [2]; ORCiD logo [3]; ORCiD logo [2]
  1. Max-Planck Institut fur Polymerforschung, Ackermannweg, Mainz (Germany); Univ. Federal do Rio Grande do Sul, Porto Alegre (Brazil)
  2. Max-Planck Institut fur Polymerforschung, Ackermannweg, Mainz (Germany)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1260415
Report Number(s):
LA-UR-15-28326; JCPSA6
Journal Information:
Journal of Chemical Physics, Vol. 144, Issue 17; ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 18 works
Citation information provided by
Web of Science

References (40)

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back journal January 2009
Multiscale simulation of soft matter systems journal January 2010
Perspective: Coarse-grained models for biomolecular systems journal September 2013
Interatomic Potentials from First-Principles Calculations: The Force-Matching Method journal June 1994
Multiscale coarse graining of liquid-state systems journal October 2005
Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach journal October 1995
Systematic hierarchical coarse-graining with the inverse Monte Carlo method journal December 2015
Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates journal February 1998
Simulation of polymer melts. II. From coarse-grained models back to atomistic description journal February 1998
Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations journal August 2003
The relative entropy is fundamental to multiscale and inverse thermodynamic problems journal October 2008
Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations journal February 2009
Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions journal May 2011
A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition journal December 2013
Water Modeled As an Intermediate Element between Carbon and Silicon journal April 2009
The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations journal July 2007
Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? journal January 2009
Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids journal December 2015
Coil–Globule–Coil Transition of PNIPAm in Aqueous Methanol: Coupling All-Atom Simulations to Semi-Grand Canonical Coarse-Grained Reservoir journal November 2013
Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA journal July 2015
Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly journal December 2005
Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir journal April 2012
Kirkwood–Buff Analysis of Liquid Mixtures in an Open Boundary Simulation journal February 2012
The Statistical Mechanical Theory of Solutions. I journal June 1951
Preferential Solvation of Triglycine in Aqueous Urea: An Open Boundary Simulation Approach journal March 2012
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit journal February 2013
A Kirkwood−Buff Derived Force Field for Mixtures of Urea and Water journal April 2003
The missing term in effective pair potentials journal November 1987
Principles that Govern the Folding of Protein Chains journal July 1973
Molecular dynamics with coupling to an external bath journal October 1984
A smooth particle mesh Ewald method journal November 1995
LINCS: A linear constraint solver for molecular simulations journal September 1997
Kirkwood–Buff Coarse-Grained Force Fields for Aqueous Solutions journal April 2012
Representability and Transferability of Kirkwood–Buff Iterative Boltzmann Inversion Models for Multicomponent Aqueous Systems journal November 2013
Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions journal February 2012
Thermodynamics of aqueous urea solutions journal January 1967
Activity and Activity Coefficient of Water in Aqueous Solutions and Their Relationships with Solution Structure Parameters journal January 1997
Predicting the energetics of osmolyte-induced protein folding/unfolding journal October 2005
VMD: Visual molecular dynamics journal February 1996
Md Simulation Trajectory And Related Files For Dmpc Bilayer, Högberg Et Al, J.Comp.Chem., 29, 2359 (2008) dataset January 2015

Cited By (4)

Adaptive resolution simulation of oligonucleotides journal December 2016
Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining journal September 2019
Comparison of iterative inverse coarse-graining methods journal October 2016
MARTINI-based Coarse-grained Model for Poly(alpha-peptoid)s preprint January 2019