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This paper describes 3 classes of parallel algorithms suitable for short-range MD force fields: so-called atom-, force-, and spatial-decomposition algorithms.
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Parallel computer programs are used to speed up the calculation of computationally demanding scientific problems such as MD simulations. Parallel MD methods ...
In a recent article, a new algorithm for the parallelization of MD simulations on SMP systems has been proposed [5]. The cell task method uses task-based ...
A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro)molecules in aqueous environment is described.
Apr 5, 2024 · Parallel cascade selection molecular dynamics (PaCS-MD) is an enhanced conformational sampling method conducted as a “repetition of time leaps ...
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○ Molecular dynamics (MD) is a very versatile research tool with ... Flow of a parallel MD program. ○ Update velocities to v(t+∆t/2). ○ Update ...
The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decomposition combined with force decomposition to enhance ...
Nov 16, 2020 · In this paper, we address high performance extreme-scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular-scale ...
Ready to use analysis and buildings blocks to write parallel analysis algorithms using MDAnalysis with Dask.
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
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