TNAMD: Implementation of TIGER2 in NAMD

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.Program summaryProgram title: TNAMDCatalogue identifier: AEHH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 24 837No. of bytes in distributed program, including test data, etc.: 610 107Distribution format: tar.gzProgramming language: Tcl 8.5Computer: Clusters, workstations. Tested on Intel Clovertown, Atom.Operating system: Linux, Windows (with Linux shell)Has the code been vectorised or parallelised?: Yes. Parallelised with MPIClassification: 3External routines: NAMD 2.6 (http://www.ks.uiuc.edu/Research/namd/)Nature of problem: Replica-exchange molecular dynamics.Solution method: Replicas are assigned to unique processes, and pass through a series of cycles of heating, equilibration, quenching and sampling; after which temperatures are swapped between replicas.Running time: The test run can take up to twenty minutes.