MD Engines

GENESIS contains two MD engines, atdyn and spdyn, having different system decomposition schemes.

  • atdyn: atomic decomposition dynamics.
    • small system (< 10,000 atoms approximately)
    • coarse-grained simulations
    • vacuum condition
  • spdyn: spatial decomposition dynamics.
    • larger system (> 10,000 atoms approximately) in periodic boundary condition
    • use GPU

For basic simulations (such as proteins in solution or in membrane), performance of spdyn is much better than atdyn. Please use atdyn only in the cases listed above. Please note that spdyn won’t run for very small systems due to the limitation of the decomposition scheme. (The minimum possible size might be determined by system size and pairlist length.)