Optimized explicit-solvent replica exchange molecular dynamics from scratch
Document Type
Article
Publication Date
8-28-2008
Department
Department of Physics
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)
Publication Title
Journal of Physical Chemistry B
Recommended Citation
Nadler, W.,
&
Hansmann, U.
(2008).
Optimized explicit-solvent replica exchange molecular dynamics from scratch.
Journal of Physical Chemistry B,
112(34), 10386-10387.
http://doi.org/10.1021/jp805085y
Retrieved from: https://digitalcommons.mtu.edu/michigantech-p/8126