Adaptive resolution simulations of biomolecular systems

Review

Abstract

In this review article, we discuss and analyze some recently developed hybrid atomistic–mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping—i.e., one coarse-grained bead represents one water molecule—for development of a multiscale salt solution model. In order to make use of coarse-grained molecular models that are compatible with the MARTINI force field, one has to resort to a supramolecular mapping, in particular to a 4-to-1 mapping, where four water molecules are represented with one coarse-grained bead. To this end, bundled atomistic water models are employed, i.e., the relative movement of water molecules that are mapped to the same coarse-grained bead is restricted by employing harmonic springs. Supramolecular coupling has recently also been extended to polarizable coarse-grained water models with explicit charges. Since these coarse-grained models consist of several interaction sites, orientational degrees of freedom of the atomistic and coarse-grained representations are coupled via a harmonic energy penalty term. The latter aligns the dipole moments of both representations. The reviewed multiscale solvent models are ready to be used in biomolecular simulations, as illustrated in a few examples.

Keywords

Molecular dynamics Adaptive resolution Supramolecular coupling 

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Copyright information

© European Biophysical Societies' Association 2017

Authors and Affiliations

  1. 1.Department of Molecular ModelingNational Institute of ChemistryLjubljanaSlovenia
  2. 2.Department of Physics, Faculty of Mathematics and PhysicsUniversity of LjubljanaLjubljanaSlovenia
  3. 3.Chair of Computational ScienceETH ZurichZurichSwitzerland

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