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Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support experimental measures at both constant redox potential and pH is very important. Such computational techniques have the potential to validate experimental observations performed under these conditions and to provide additional information unachievable experimentally such as an atomic level description of macroscopic measures. We present the implementation of discrete redox and protonation states methods for constant redox potential Molecular Dynamics (CEMD), for coupled constant pH and constant redox potential MD (C(pH,E)MD), and for Replica Exchange MD along the redox potential dimension (E-REMD) on the AMBER software package. Validation results are presented for a small system that contains a single heme group: N-acetylmicroperoxidase-8 (NAcMP8) axially connected to a histidine peptide. The methods implemented allow one to make standard redox potential (Eo) predictions with the same easiness and accuracy as pKa predictions using the constant pH molecular dynamics and pH-REMD methods currently available on AMBER. In our simulations, we can correctly describe, in agreement also with theoretical predictions, the following behaviors: when a redox-active group is reduced, the pKa of a near pH-active group increases because it becomes easier for a proton to be attached; equivalently, when a pH-active group is protonated, the Eo of an adjacent redox-active group rises. Furthermore, our results also show that E-REMD is able to achieve faster statistical convergence than CEMD or C(pH,E)MD. Moreover, computational benchmarks using our methodologies show high-performance of GPU accelerated calculations in comparison to conventional CPU calculations.
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information that cann
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects,
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had previousl
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that different replic
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. The next set