TNAMD: Implementation of TIGER2 in NAMD

William J. Menz; Matthew J. Penna; Mark J. Biggs

doi:10.1016/j.cpc.2010.09.011

TNAMD: Implementation of TIGER2 in NAMD

William J. Menz, Matthew J. Penna, Mark J. Biggs

University Executive

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	2082-2085
Number of pages	4
Journal	Computer Physics Communications
Volume	181
Issue number	12
DOIs	https://doi.org/10.1016/j.cpc.2010.09.011
Publication status	Published - Dec 2010

Keywords

Free energy prediction
Molecular dynamics
NAMD
Replica-exchange molecular dynamics
TIGER2 method
Tool command language

ASJC Scopus subject areas

Hardware and Architecture
General Physics and Astronomy

Access to Document

10.1016/j.cpc.2010.09.011

Cite this

@article{ca4aeea6deaf4f9a958d781ceefd6a69,

title = "TNAMD: Implementation of TIGER2 in NAMD",

abstract = "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.",

keywords = "Free energy prediction, Molecular dynamics, NAMD, Replica-exchange molecular dynamics, TIGER2 method, Tool command language",

author = "Menz, {William J.} and Penna, {Matthew J.} and Biggs, {Mark J.}",

year = "2010",

month = dec,

doi = "10.1016/j.cpc.2010.09.011",

language = "English",

volume = "181",

pages = "2082--2085",

journal = "Computer Physics Communications",

issn = "0010-4655",

publisher = "Elsevier",

number = "12",

}

TY - JOUR

T1 - TNAMD

T2 - Implementation of TIGER2 in NAMD

AU - Menz, William J.

AU - Penna, Matthew J.

AU - Biggs, Mark J.

PY - 2010/12

Y1 - 2010/12

N2 - 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.

AB - 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.

KW - Free energy prediction

KW - Molecular dynamics

KW - NAMD

KW - Replica-exchange molecular dynamics

KW - TIGER2 method

KW - Tool command language

UR - http://www.scopus.com/inward/record.url?scp=77957924051&partnerID=8YFLogxK

U2 - 10.1016/j.cpc.2010.09.011

DO - 10.1016/j.cpc.2010.09.011

M3 - Article

AN - SCOPUS:77957924051

SN - 0010-4655

VL - 181

SP - 2082

EP - 2085

JO - Computer Physics Communications

JF - Computer Physics Communications

IS - 12

ER -

TNAMD: Implementation of TIGER2 in NAMD

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this