SBGridTV

Supported Applications

ACEMD

  • Description

    ACEMD is heavily optimized molecular dynamics (MD) engine specially designed to run on NVIDA GPUs. ACEMD is extremely fast (115ns/day for DHFR using 1 GPU) and allows performing MD simulations on the microsecond scale in a single workstation. ACEMD is a fully featured platform (PME, NPT, NVT, TCL, PLUMED, CAMSHIFT), that can read CHARMM/NAMD and AMBER input files. Furthermore, ACEMD works with CUDA and OpenCL and uses similar syntax to other MD software. ACEMD has been validated by numerous studies and powers GPUGrid, one of the largest distributed computing projects worldwide. Parallel, fully supported versions of ACEMD are available through Acellera.

  • References

    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