ACEMD最领先的分子动力学GPU软件

ACEMD是一个功能全面的的分子动力学模拟软件包，可以高效的运行于NVIDIA GPU上。ACEMD的主要优势是对分子动力学模拟，大大提高模拟效率（几十甚至上百倍），提高科研效率。


ACEMD的主要功能及特点

  1. 全面覆盖Amber、CHARMM、NAMD、CellMD、Gromos功能
  2. 部分覆盖LAMMPS、Gromacs的功能
  3. 包含Particle mesh Ewald (PME)及广义反应力场
  4. 方便读取Charmm、Amber等力场
  5. 支持metadynamics, steered MD等插件
  6. 支持umbrella sampling, replica exchange等插件
  7. 运行时间步长超过4fs
  8. 刚性、柔性氢键
  9. 完全兼容CUDA、OpenCL
  10. 支持TCL脚本
  11. 便于根据模拟结果不断修改模拟条件
  12. 很好的稳定性、可靠性

 

性能对比

ACEMD1

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.

 

ACEMD2

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