Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?
Open Access
- 14 January 2009
- journal article
- Published by Springer Nature in The European Physical Journal E
- Vol. 28 (2), 221-229
- https://doi.org/10.1140/epje/i2008-10413-5
Abstract
We employ the inverse Boltzmann method to coarse-grain three commonly used three-site water models (TIP3P, SPC and SPC/E) where one molecule is replaced with one coarse-grained particle with isotropic two-body interactions only. The shape of the coarse-grained potentials is dominated by the ratio of two lengths, which can be rationalized by the geometric constraints of the water clusters. It is shown that for simple two-body potentials either the radial distribution function or the geometrical packing can be optimized. In a similar way, as needed for multiscale methods, either the pressure or the compressibility can be fitted to the all atom liquid. In total, a speed-up by a factor of about 50 in computational time can be reached by this coarse-graining procedure.Keywords
This publication has 43 references indexed in Scilit:
- Coarse-Graining in Interaction Space: A Systematic Approach for Replacing Long-Range Electrostatics with Short-Range PotentialsThe Journal of Physical Chemistry B, 2008
- Concurrent triple-scale simulation of molecular liquidsThe Journal of Chemical Physics, 2008
- Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostatSoft Matter, 2007
- Solvation free energies of amino acid side chain analogs for common molecular mechanics water modelsThe Journal of Chemical Physics, 2005
- Adsorption of Water Molecules on Flat and Stepped Nickel Surfaces from First PrinciplesJournal of Chemical Theory and Computation, 2004
- On Coarse-Graining by the Inverse Monte Carlo Method: Dissipative Particle Dynamics Simulations Made to a Precise Tool in Soft Matter ModelingSoft Materials, 2002
- Solvent Structure, Dynamics, and Ion Mobility in Aqueous Solutions at 25 °CThe Journal of Physical Chemistry B, 1998
- Simulating Microscopic Hydrodynamic Phenomena with Dissipative Particle DynamicsEurophysics Letters, 1992
- Interaction Models for Water in Relation to Protein HydrationPublished by Springer Nature ,1981
- A Theory of Water and Ionic Solution, with Particular Reference to Hydrogen and Hydroxyl IonsThe Journal of Chemical Physics, 1933