User:Mjharvey2/sandbox
| Developer(s) | Multiscale Lab, UPF, PRBB and Acellera Ltd |
|---|---|
| Initial release | 2009 |
| Stable release | 3212u1
/ Sept 2013 |
| Operating system | Linux |
| Available in | CUDA |
| License | Proprietary software |
| Website | www.acellera.com/products/acemd |
ACEMD [1] is a molecular dynamics simulation package written in the Cuda language for NVIDIA General Purpose GPUs. It was developed at the Multiscale Lab within the Department of Experimental and Health Sciences, UPF, hosted at the Barcelona Biomedical Research Park. ACEMD is available under commercial license from Acellera Ltd. A limited version, ACEMD Basic, is available free-of-charge [2] for academic and industrial use.
A derivative of ACEMD is used as the computational engine of the volunteer distributed computing project GPUGRID.
Features
[edit]ACEMD is designed specifically for NVIDIA General Purpose GPUs, such as the Tesla and GeForce ranges. As a consequence, it cannot be run on CPU-only platforms.
Reflecting the research interests of the original developers, ACEMD is optimised for simulation of biomolecular systems within an explicit solvent, and parameterised with Amber, CHARMM and OPLS force fields.
ACEMD contains a GPU implementation[3] of the Smooth Particle-mesh Ewald summation treatment of long-range electrostatics.
Integration is performed using the velocity-Verlet algorithm. The M-Shake and RATTLE[4] algorithms are used for imposing constraints on fast modes of vibration, which, in conjunction with hydrogen mass repartioning [5]
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See also
[edit]References
[edit]- ^ "ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale".
- ^ [1]
- ^ "An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware".
- ^ "A velocity version of the shake algorithm for molecular dynamics calculations".
- ^ "Improving efficiency of large time scale molecular dynamics simulations of hydrogen-rich systems" (PDF).
External links
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