TNAMD: Implementation of TIGER2 in NAMD

摘要

Replica-exchange molecular dynamics (REMD) must be used to enhance sampling when there are significant (relative to kT) barriers between different parts of the phase space. TIGER2 is a next-generation REMD method that offers more efficient sampling compared to the original REMD method by reducing the number of replicas required to span a given temperature range. In this paper, we present an implementation of the TIGER2 algorithm in the NAMD software package. This implementation exploits the capacity of NAMD to interpret Tcl scripts. The Tcl script implementing TIGER2 is provided and explained in detail, and demonstrated for alanine dipeptide in water.