ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

By M. Harvey, Giovanni Giupponi, G. de Fabritiis. Journal of Chemical Theory and Computation, 2009

876 citations recorded by the source corpus.

The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class biomolecular dynamics (MD) engine supporting CHARMM and AMBER force fields. Designed specifically for GPUs it is able to achieve supercomputing scale performance of 40 ns/day for all-atom protein systems with over 23 000 atoms. We provide a validation and performance evaluation of the code and run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. We believe that microsecond time scale molecular dynamics on cost-effective hardware will have important methodological and scientific implications.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7fcd5fe69ddd9ba4175c95c71fa6e04dfa4e483b

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Citations in the corpus

Multiensemble Markov models of molecular thermodynamics and kinetics (2016, neutral): “exp h f k j − f k i i vj + v k i , [18]”
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations (2011, methodology): “Voelz VA, Bowman GR, Beauchamp K, Pande VS (2010) Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).”
Identification of slow molecular order parameters for Markov model construction. (2013, methodology): “We have performed 7706 all-atom explicit-solvent simulations of 24 ns each using the ACEMD software [29] on the GPUGRID distributed computing platform [12], yielding a total 168 μs simulation data.”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, background): “…development of code able to exploit the speed of GPUs (Graphics Processing Units), which has given access to tera-scale performances with the use of a common workstation, and a consequent relatively low cost (Van Meel et al., 2008; Friedrichs et al., 2009; Harvey et al., 2009; Nobile et al., 2017).”
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics (2020, methodology): “To prevent this, a minimization step with chiral restraints is now performed in NAMD ahead of unrestrained minimization in the program AceMD as previously described.”
GPU-Accelerated Molecular Modeling Coming Of Age (2010, positive): “Released as a commercially licensed biomolecular dynamics software package, ACEMD 8 is explicitly designed for execution by a single workstation with multiple GPUs [52].”