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      Interaction-component analysis of the hydration and urea effects on cytochrome c

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          Comparison of simple potential functions for simulating liquid water

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            GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

            Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.
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              A smooth particle mesh Ewald method

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                Author and article information

                Journal
                JCPSA6
                The Journal of Chemical Physics
                J. Chem. Phys.
                AIP Publishing
                0021-9606
                1089-7690
                February 28 2016
                February 28 2016
                February 23 2016
                : 144
                : 8
                : 085102
                Affiliations
                [1 ]Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
                [2 ]RIKEN Quantitative Biology Center, Kobe, Hyogo 650-0047, Japan
                [3 ]Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8568, Japan
                [4 ]Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
                Article
                10.1063/1.4941945
                © 2016
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