Optimized explicit-solvent replica exchange molecular dynamics from scratch

Document Type

Article

Publication Date

8-28-2008

Abstract

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) ≈ 1 + 0.594√C In(T max/Tmin), where C is the specific heat, and the temperatures distributed according to Ti(opt) ≈ T min (Tmax/Tmin)(i-1)/(N-1). © 2008 American Chemical Society.

Publication Title

Journal of Physical Chemistry B

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