Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.

摘要: A necessary step to properly assess and validate the performance of force fields for biomolecules is exhaustively sample accessible conformational space, which challenging large RNA structures. Given questions regarding reliability modeling structure dynamics with current methods, we have begun use tetranucleotides evaluate fields. These systems, though small, display considerable variability complete sampling standard simulation methods remains challenging. Here compare discuss known variations replica exchange molecular (REMD) specifically temperature REMD (T-REMD), Hamiltonian (H-REMD), multidimensional (M-REMD) been implemented in Amber’s accelerated GPU code. Using two independent simulations, show that M-REMD not only makes very efficient emerging large-scale clusters, like Blue Waters at University Illinois, but also critically...