Implementation of replica-exchange umbrella sampling in GAMESS

Shingo Ito, Dmitri G. Fedorov, Yuko Okamoto, Stephan Irle

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

In GAMESS-US quantum chemistry package, both replica-exchange molecular dynamics (REMD) and the umbrella sampling (US) methods are available. However, prior to this work, the replica-exchange umbrella sampling (REUS) method, combining REMD and US, was not implemented. REUS affords a more efficient conformational sampling than the conventional US method and is often used in MD simulations. We implemented REUS in GAMESS-US and improved some routines of the existing REMD code. A density-functional tight-binding REMD (DFTB-REMD) simulation of alanine deca-peptide and a DFTB-MD REUS simulation of proton transfer in malonaldehyde were performed. The results of DFTB-MD REUS simulations performed with three different simulation packages were compared to validate our GAMESS-US implementation.

Original languageEnglish
Pages (from-to)152-162
Number of pages11
JournalComputer Physics Communications
Volume228
DOIs
StatePublished - Jul 2018

Keywords

  • Density-functional tight-binding
  • GAMESS-US
  • Multidimensional replica-exchange method
  • Replica-exchange molecular dynamics
  • Replica-exchange umbrella sampling
  • Umbrella sampling

Fingerprint

Dive into the research topics of 'Implementation of replica-exchange umbrella sampling in GAMESS'. Together they form a unique fingerprint.

Cite this