Polarizable Mean-Field Model of Water for Biological Simulations with AMBER and CHARMM Force Fields

Citations Over TimeTop 15% of 2012 papers

Abstract

Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified since then. The reason is that the non-polarizable force fields that are mostly used to describe proteins and other biological molecules are incompatible with more sophisticated modern polarizable models of water. The issue is electronic polarizability: in liquid state, in protein, and in vacuum the water molecule is polarized differently, and therefore has different properties; thus the only way to describe all these different media with the same model is to use a polarizable water model. However, to be compatible with the force field of the rest of the system, e.g. a protein, the latter should be polarizable as well. Here we describe a novel model of water that is in effect polarizable, and yet compatible with the standard non-polarizable force fields such as AMBER, CHARMM, GROMOS, OPLS, etc. Thus the model resolves the outstanding problem of incompatibility.

Related Papers

• → A molecular dynamics study of polarizable water(1989)410 cited
• → Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers(2009)68 cited
• → Secondary structure dependence of amyloid‐β(1–40) on simulation techniques and force field parameters(2021)24 cited
• → Effects of the polarizability and water density constraint on the structure of water near charged surfaces: Molecular dynamics simulations(2000)33 cited
• → Model Dependence of the Electrostatic Response to a Molecular-Sized Ion in Water(2012)3 cited