Paper Citing NAMD - Abstract
Iori, F.; Corni, S.
Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1656-1666, JUL 30 2008
Combinatorial bio-techniques have demonstrated that proteins can be good and even selective binders for several inorganic surfaces, including metals. However, the understanding of the basic physical mechanisms that govern such interactions did not keep up with the success in these experiments. The comprehension of such mechanisms would greatly benefit from the computational investigation of the problem. Because of the complexity of the system, classical molecular dynamics simulations based on an atomistic description appear to be the best compromise between reliability and feasibility. For proteins interacting with metal surfaces, however, methodological improvements with respect to standard Molecular Dynamics (MD) of proteins are needed, since the polarization of the metal induced by the protein (and the surrounding water) is not generally negligible. In this article, we present a simple approach to introduce metal polarization effects (often termed image effects) in MD simulations by exploiting standard features of bio-oriented MD codes such as the widely used GROMACS and NAMD. Tests to show the reliability of the proposed methods are presented, and the results for a model application showing the importance of image effects are also discussed. (C) 2008 Wiley Periodicals, Inc.
