SBGridTV

Supported Applications

ACEMD

  • Description

    a heavily optimized molecular dynamics (MD) engine specially designed to run on NVIDA GPUs. It is extremely fast (115ns/day for DHFR using 1 GPU) and performs MD simulations on the microsecond scale in a single workstation. ACDMD can read CHARMM/NAMD and AMBER input files, works with CUDA and OpenCL, and uses similar syntax to other MD software.

  • Primary Citation

    Harvey MJ, Giupponi G, De Fabritiis G. ACEMD: Accelerating biomolecular dynamics in the microsecond time scale, J. Chem. Theory and Comput. 5, 1632 (2009). DOI: 10.1021/ct9000685

    Harvey MJ, De Fabritiis G. An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware, J. Chem. Theory Comput., 5, 2371–2377 (2009). DOI: 10.1021/ct900275y

    Buch I, Giorgino T, De Fabritiis G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10184-9. doi: 10.1073/pnas.1103547108. Epub 2011 Jun 6. PMID: 21646537 PMCID: PMC3121846