Optimized explicit-solvent replica exchange molecular dynamics from scratch.
Replica exchange molecular dynamics (REMD) simulations have become an important tool to study proteins and other biological molecules in silico. However, such investigations require considerable, and often prohibitive, numerical effort when the molecules are simulated in explicit solvents. In this communication we show that in this case the cost can be minimized by choosing the number of replicas as N(opt) approximately 1+0.594 radical C ln(Tmax/Tmin), where C is the specific heat, and the temperatures distributed according to Ti(opt) approximately T min(Tmax/Tmin)(i-1)/(N-1).
Nadler
Walter
W
John-von-Neumann Institute for Computing, Forschungszentrum Julich, D-52425 Julich, Germany. wnadler@fz-juelich.de
Hansmann
Ulrich H E
UH
D000465:Algorithms; D003198:Computer Simulation; D006358:Hot Temperature; D008958:Models, Molecular; D009010:Monte Carlo Method; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013696:Temperature
D011506:Proteins; D012997:Solvents