ACEMD: High performance molecular dynamics

ACEMD is a bio-molecular dynamics (MD) software reading CHARMM(NAMD) and AMBER formats, designed to run on Nvidia^® graphics processing units (GPUs) in order to reach microsecond simulation times.

• ACEMD resources at multiscalelab (Manual Pdf)
• ACEMD details
• Acellera MetroCubo solutions: hardware and software

Download a functional version of ACEMD for testing. Only TCL scripting and dcd output are disabled. Requirements: Linux 64-bit. A modern NVIDIA graphic card (GT8800 or cards from GT 9000, GT 200 and Tesla10 devices). The NVIDIA CUDA driver installed.

Validation

A detailed, peer-reviewed paper on ACEMD features, benchmark and validation has been published on the Journal of Chemical Theory and Computation. Here

Performance (nanoseconds /day)

Hardware used: NVIDA GTX280/TESLA C1070 GPUs (ACEMD) and 8 CPU cores for data of other MD programs.

Test system: Dihydrofolate reductase (DHFR) solvated in water, 23558 atoms. Periodic boundary conditions, 9 Å cutoff, PME for long range electrostatic, heavy hydrogens, rigid bonds, time step 2fs NAMD, 2.5fs DESMOND, 4fs GROMACS and ACEMD.

ACEMD pricing

For pricing information, support and consulting on ACEMD solutions for industries and non-academic organizations, please contact sales@acellera.com.

Product	Price (euros)	Subscription	Description
ACEMD 4 GPUs	1600 &euro	academic license	Single node, serial up to 4 GPU devices Manual, demos, support
ACEMD PRO PARALLEL	Please contact sales@acellera.com	academic and industrial licenses	Single to many nodes Parallel on multiple GPUs Manual, demos, plugins, support and updates
Discounts are available for multiple licenses and additional subscription periods, please contact sales@acellera.com. Upgrades of version are also possible.

Feature list

• ACEMD is available for Windows XP, Vista (32 and 64 bit) and all Linux 64 distributions
• Input/output files compatibles with NAMD (pdb, psf, coor, parameter file, dcd, many configuration parameters)
• Read CHARMM and Amber formats
• TCL scripting available for advanced jobs handling
• Long time steps up to 4 fs (hydrogen mass repartitioning)
• Rigid and harmonic hydrogen bonds
• Langevin thermostatting
• Particle mesh Ewald (PME) for long range electrostatics
• Steered molecular dynamics and umbrella sampling simulations
• Metadynamics free energy calculations
• Compatible with VMD and other visualization packages
• Example simulations with inputs and molecular structures
• Molecular structure creation via VMD
• A forum for users
• Effective manual pages
• Robustness. ACEMD is the MD engine behind www.gpugrid.net