Affiliation:
1. College of Chemistry, Nankai University , Tianjin 300071, China
2. Laboratoire International Associé CNRS and University of Illinois at Urbana−Champaign, UMR n°7019, Université de Lorraine , BP 70239, F-54506 Vandœuvre-lès-Nancy, France
Abstract
On general-purpose hardware, the timescale amenable to molecular dynamics (MD) simulations is usually microseconds. When investigating rare events that fall beyond the scope of MD, one possible way to boost up the exploration, or sampling, of the configurational space consists in using enhanced-sampling algorithms. In this chapter, we introduce the theoretical background of popular enhanced sampling techniques based on collective variables (CVs), such as umbrella sampling, adaptive biasing force, metadynamics and their variants. We then provide a step-by-step protocol to illustrate how to carry out an enhanced-sampling simulation to capture the rare events by means of MD simulations. The use of both the Colvars (supported by NAMD, LAMMPS and Gromacs) and Plumed (supported by NAMD, LAMMPS, Gromacs, Amber, OpenMM, etc.) modules to carry out CV-based enhanced-sampling simulations is introduced. Finally, we discuss the matters that require attention in the practical study of coupled movements in complex (bio)chemical molecular objects.
Publisher
AIP Publishing LLCMelville, New York