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ACEMD最領先的分子動力學GPU軟件

ACEMD是一個功能全面的的分子動力學模擬軟件包，可以高效的運行于NVIDIA GPU上。ACEMD的主要優勢是對分子動力學模擬，大大提高模擬效率（幾十甚至上百倍），提高科研效率。

ACEMD的主要功能及特點

1. 全面覆蓋Amber、CHARMM、NAMD、CellMD、Gromos功能
2. 部分覆蓋LAMMPS、Gromacs的功能
3. 包含Particle mesh Ewald (PME)及廣義反應力場
4. 方便讀取Charmm、Amber等力場
5. 支持metadynamics, steered MD等插件
6. 支持umbrella sampling, replica exchange等插件
7. 運行時間步長超過4fs
8. 剛性、柔性氫鍵
9. 完全兼容CUDA、OpenCL
10. 支持TCL腳本
11. 便于根據模擬結果不斷修改模擬條件
12. 很好的穩定性、可靠性

 

性能對比

Fermi is a GTX580 GPU. Kepler is a GTX680 GPU. Tesla is a M2090. ECC o. CUDA4.2 and ACEMD ver 2400. DHFR, dihydrofolate reductase solvated in water, 23558 atoms, periodic boundary conditions, 9 A cuto, PME long range electrostatic 64×64x64, hydrogen mass repartitioning, rigid bonds, Langevin thermostat, time step 4 fs. Time step 2 fs NAMD and AMBER, 2.5 fs DESMOND and 4 fs GROMACS. AMBER 8 A cuto.
Source DESMOND: http://www.hpcadvisorycouncil.com/pdf/Desmond.pdf.
Source GROMACS: Hess B., et al. J Chem Theory Comput 2008, 4 (2): 435. doi:10.1021/ct700301q.
Source NAMD: https://www.teragrid.org/web/usersupport/namd_benchmark.

 

Fermi is a GTX580 GPU. Kepler is a GTX680 GPU. Tesla is a M2090. ECC o. CUDA4.2 and ACEMD ver 2400. DHFR, dihydrofolate reductase solvated in water, 23558 atoms, periodic boundary conditions, 9 A cuto, PME long range electrostatic 64×64x64, hydrogen mass repartitioning, rigid bonds, Langevin thermostat, time step 4 fs. Time step 2 fs NAMD and AMBER, 2.5 fs DESMOND and 4 fs GROMACS. AMBER uses 8 A cuto.
Source AMBER: http://ambermd.org/gpus/benchmarks.htm
Source GROMACS: http://www.gromacs.org/Downloads/Installation_Instructions/GPUs
Source NAMD: Acellera