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

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

JOURNAL OF CHEMICAL PHYSICS, cilt.143, sa.22, 2015 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 143 Sayı: 22
  • Basım Tarihi: 2015
  • Doi Numarası: 10.1063/1.4936968
  • Dergi Adı: JOURNAL OF CHEMICAL PHYSICS
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Hacettepe Üniversitesi Adresli: Evet

Özet

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.