Replica-exchange-with-tunneling for fast exploration of protein landscapes

YAŞAR F., Bernhardt N. A., Hansmann U. H. E.

JOURNAL OF CHEMICAL PHYSICS, vol.143, no.22, 2015 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 143 Issue: 22
  • Publication Date: 2015
  • Doi Number: 10.1063/1.4936968
  • Journal Name: JOURNAL OF CHEMICAL PHYSICS
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Hacettepe University Affiliated: Yes

Abstract

While the use of replica-exchange molecular dynamics in protein simulations has become ubiquitous, its utility is limited in many practical applications. We propose to overcome some shortcomings that hold back its use in settings such as multi-scale or explicit solvent simulations by integrating ideas of hybrid MC/MD into the replica-exchange protocol. This Replica-Exchange-with-Tunneling method is tested by simulating the Trp-cage protein, a system often used in molecular biophysics for testing sampling techniques. (C) 2015 AIP Publishing LLC.