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A nontoxic pain killer designed by modeling of pathological receptor conformations

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      A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding

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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
            Science
            Science
            American Association for the Advancement of Science (AAAS)
            0036-8075
            1095-9203
            March 02 2017
            March 02 2017
            : 355
            : 6328
            : 966-969
            10.1126/science.aai8636
            © 2017

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