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 of simulation parameters are based upon the outcome of the exchanges. Typically RE functionality is integrated into the molecular simulation software package. A primary motivation of the tight integration of RE functionality with simulation codes has been performance. This is limiting at multiple levels. First, advances in the RE methodology are tied to the molecular simulation code. Consequently these advances remain confined to the molecular simulation code for which they were developed. Second, it is difficult to extend or experiment with novel RE algorithms, since expertise in the molecular simulation code is typically required. In this paper, we propose the RepEx framework which address these aforementioned shortcomings of existing approaches, while striking the balance between flexibility (any RE scheme) and scalability (tens of thousands of replicas) over a diverse range of platforms. RepEx is designed to use a pilot-job based runtime system and support diverse RE Patterns and Execution Modes. RE Patterns are concerned with synchronization mechanisms in RE simulation, and Execution Modes with spatial and temporal mapping of workload to the CPU cores. We discuss how the design and implementation yield the following primary contributions of the RepEx framework: (i) its ability to support different RE schemes independent of molecular simulation codes, (ii) provide the ability to execute different exchange schemes and replica counts independent of the specific availability of resources, (iii) provide a runtime system that has first-class support for task-level parallelism, and (iv) required scalability along multiple dimensions.
REPDSTR module of the CHARMM: Ref. @cite_16 presents an implementation of a 2D US H-REMD method, implemented in REPDSTR module of the CHARMM @cite_25 . REPDSTR uses an MPI level parallel parallel mode where to each replica are assigned multiple MPI processes and dedicated I O routines. To improve sampling efficiency, exchange attempts are performed alternatively along the two dimensions.
@cite_16 @cite_25
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An extremely scalable computational strategy is described for calculations of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian molecular dynamics replica-exchange (H-REMD) algorithm to enhance the sampling of each simulation. In the present application, US H-REMD is carried out in a two-dimensional (2D) space and exchanges are attempted alternatively along the two axes corresponding to the two order parameters. The US H-REMD strategy is implemented on the basis of parallel parallel multiple copy protocol at the MPI level, and therefore can fully exploit computing power of large-scale supercomputers. Here the novel technique is illustrated using the leadership supercomputer IBM Blue Gene P with an application to a typical biomolecular calculation of general interest, namely the binding of calcium ions to the ... CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.