Eur. Phys. J. Special Topics 224, 2515-2518 (2015)
https://doi.org/10.1140/epjst/e2015-02537-1

Regular Article

The trees and the forest

Aims and objectives of molecular dynamics simulations

¹ Department of Physics, University of Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Roma, Italy
School of Physics, University College Dublin, Dublin, Ireland
² Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA

^a e-mail: giovanni.ciccotti@roma1.infn.it
^b e-mail: eve2@cims.nyu.edu

Received: 22 June 2015
Revised: 17 July 2015
Published online: 21 September 2015

Abstract

This comment presents few reflections, inspired by various contributions in this special issue, that address the issue of how to interpret and use molecular dynamics (MD). It is argued that, in spite of what its name seems to suggest, MD is not a tool to predict deterministic behaviors but a device to sample both time-independent and time-dependent statistical mechanics properties of molecular systems. Therefore MD simulations must be used in concert with tools from stochastic processes theory and a big challenge is how to develop these tools to make them appropriate both conceptually and practically in the context of these simulations.