The CUMULUS coarse graining method: transferable potentials for water and solutes.

Molecular dynamics (MD) simulations are an important tool for studying various interesting phenomena in nature at the molecular level. To allow molecular simulation methods to be applied to larger systems and for longer time scales, coarse grained (CG) models have been developed in which groups of atoms are represented by a single coarse grained particle. In so-called multiscale CG models, an atomistic simulation is coarse grained and subsequently used to derive a CG force field. Existing multiscale methods represent either (parts of) molecules as a single CG particle, or groups of molecules of fluctuating size as a single CG particle. Here, a novel method is introduced to coarse grain an atomistic simulation, the CUMULUS coarse graining method. In this method, CG particles have a unique, fixed composition. This important feature of our coarse graining method, which is not available in the current methods, provides a systematic method to include CG solute particles in solutions of salts in water. Combined with the iterative Boltzmann inversion procedure, our coarse graining method is employed to derive CG force fields for systems containing pure water, sodium chloride solutions, and water-octanol mixtures. It is found that the obtained force fields accurately reproduce the structural information from the atomistic simulations, as measured by the radial distribution functions. Furthermore, we conclude that the obtained CG force fields are transferable to systems of different composition for the systems studied here.

[1]  Timothy S. Carpenter,et al.  OmpA: gating and dynamics via molecular dynamics simulations. , 2008, Biochimica et biophysica acta.

[2]  Jim Pfaendtner,et al.  A systematic methodology for defining coarse-grained sites in large biomolecules. , 2008, Biophysical journal.

[3]  A. D. Mackie,et al.  Extension of the anisotropic united atoms intermolecular potential to amines, amides and alkanols: Application to the problems of the 2004 Fluid Simulation Challenge , 2005 .

[4]  Weis,et al.  Iterative predictor-corrector method for extraction of the pair interaction from structural data for dense classical liquids. , 1986, Physical review. A, General physics.

[5]  Alexander D. MacKerell,et al.  Development and current status of the CHARMM force field for nucleic acids , 2000, Biopolymers.

[6]  Gregory A Voth,et al.  A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.

[7]  Gregory A Voth,et al.  Effective force coarse-graining. , 2009, Physical chemistry chemical physics : PCCP.

[8]  Peter Spijker,et al.  Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems , 2010, International journal of molecular sciences.

[9]  R. C. Reeder,et al.  A Coarse Grain Model for Phospholipid Simulations , 2001 .

[10]  Wataru Shinoda,et al.  Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems , 2008, Science.

[11]  E. Vanden-Eijnden,et al.  Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain , 2007, Proceedings of the National Academy of Sciences.

[12]  Clare McCabe,et al.  On the investigation of coarse-grained models for water: balancing computational efficiency and the retention of structural properties. , 2010, The journal of physical chemistry. B.

[13]  Pep Español,et al.  Coarse-Graining of a Fluid and its Relation with Dissipative Particle Dynamics and Smoothed Particle Dynamic , 1997 .

[14]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[15]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[16]  Siewert J Marrink,et al.  Lipids on the move: simulations of membrane pores, domains, stalks and curves. , 2009, Biochimica et biophysica acta.

[17]  K. Binder,et al.  Coarse-graining dipolar interactions in simple fluids and polymer solutions: Monte Carlo studies of the phase behavior. , 2009, Physical chemistry chemical physics : PCCP.

[18]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[19]  Weis,et al.  Pair interaction from structural data for dense classical liquids. , 1985, Physical review letters.

[20]  K. Schulten,et al.  Molecular dynamics simulations of membrane channels and transporters. , 2009, Current opinion in structural biology.