Exchange frequency in replica exchange molecular dynamics.
The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.
Sindhikara
Daniel
D
Department of Physics, University of Florida, Gainesville, Florida 32611-8435, USA.
Meng
Yilin
Y
Roitberg
Adrian E
AE
D003198:Computer Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
D010455:Peptides