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Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance on platforms containing a large number of processors, but may also be executed on a single computer. The core and source code are available without cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the Folding@home distributed computing project. Desmond is available for commercial use through Schrödinger, Inc. == Desmond molecular dynamics program == Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using particle-mesh-based Ewald techniques. Constraints can be enforced using the M-SHAKE algorithm. These approaches can be used in combination with time-scale splitting (RESPA-based) integration schemes. Desmond can compute energies and forces for many standard fixed-charged force fields used in biomolecular simulations, and is also compatible with polarizable force fields based on the Drude formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (Andersen, Nosé-Hoover, and Langevin) and pressure control (Berendsen, Martyna-Tobias-Klein, and Langevin). The code also supports methods for restraining atomic positions as well as molecular configurations; allows simulations to be carried out using a variety of periodic cell configurations; and has facilities for accurate checkpointing and restart. Desmond can also be used to perform absolute and relative free energy calculations (e.g.,. free energy perturbation). Other simulation techniques (such as replica exchange) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models. There is also a GPU-accelerated version of Desmond available that is approximately 60-80 times faster than the CPU version. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Desmond (software)」の詳細全文を読む スポンサード リンク
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