Microcanonical replica exchange molecular dynamics simulation of proteins.
We present microcanonical replica exchange molecular dynamics simulations as an alternative to canonical ones. Its advantage is the easily tunable high acceptance rate for replica exchange. We present the theory, comment on its actual implementation, and demonstrate its application for a common test case, the trp-cage protein.
Kar
Parimal
P
Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA. pkar@mtu.edu
Nadler
Walter
W
Hansmann
Ulrich H E
UH
D001703:Biophysics / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D007700:Kinetics; D015233:Models, Statistical; D009010:Monte Carlo Method; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry
D011506:Proteins; D012997:Solvents