Replica Exchange Molecular Dynamics (REMD) is a state-of-the-art methodology that allows faster statistical ensemble convergence while taking advantage of computational parallelism. Regular MD simulations may take a significantly large number of steps to achieve ensemble convergence, mainly for large systems, which could make some studies impracticable. AMBER currently has a couple of REMD methods implemented, some one-dimensional (pH-REMD, T-REMD and H-REMD) and one multidimensional (H,T-REMD). On this work, we present the implementation of a new replica exchange dimension (Redox Potential) and new options for multidimensional REMD simulations (pH and Redox Potential).<br/><br/>Due to the similarity between the Henderson-Hasselbalch equation (applied to acid-base reactions) and the Nernst equation (applied to electrochemistry, reduction reactions), the mathematical derivations used on AMBER for constant pH MD and pH-REMD can be extended to the Redox Potential (represented by the letter E). This extension is important because several experimental measures are done both at constant pH and at constant E. Also, as pH and E affect the charge distribution on molecules due to changes in the predominant protonation/oxidation state of the relevant groups, these protonation/oxidation states can be related to the structure and function of proteins and other biomolecules, and it can affect properties like stability, ligand binding, catalysis, absorption spectrum, among others. Therefore, theoretical methods that can correctly describe the protonation/oxidation states at constant pH and at constant E are very important.<br/><br/>We present validation tests for the new implementations (ex.: E-REMD, pH,T-REMD, E,T-REMD and E,T,pH-REMD) and also show that our results are in agreement with theoretical and experimental expectations. All the new implementations are also available using AMBER’s accelerated GPU code. We show computational benchmarks that reveal high-performance on calculations using GPU in comparison with serial or MPI calculations for large systems, where the GPU code shows its potential to compute in hours what the serial calculation would take weeks.

High-performance multidimensional replica exchange molecular dynamics along pH, redox potential and temperature dimensions using AMBER

255th National Meeting (2018)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.