Systematic hierarchical coarse-graining with the inverse Monte Carlo method

We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulation...

Full description

Saved in:
Bibliographic Details
Published in:The Journal of chemical physics 2015-12, Vol.143 (24), p.243120-243120
Main Authors: Lyubartsev, Alexander P, Naômé, Aymeric, Vercauteren, Daniel P, Laaksonen, Aatto
Format: Article
Language:English
Subjects:
ABUNDANCE
CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS
COMPUTER CODES
Computer simulation
CONCENTRATION RATIO
DEGREES OF FREEDOM
Deoxyribonucleic acid
Distribution functions
DNA
DNA - chemistry
FLUCTUATIONS
GRAIN SIZE
Granulation
INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY
Molecular dynamics
MOLECULAR DYNAMICS METHOD
Molecular Dynamics Simulation
MONTE CARLO METHOD
Monte Carlo simulation
Physics
POTENTIALS
PROTEINS
Proteins - chemistry
Quantum Theory
Radial distribution
SALTS
SPATIAL DISTRIBUTION
System effectiveness
Variation
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730-3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.
ISSN:0021-9606
1089-7690
1089-7690
DOI:10.1063/1.4934095