ACEMD is a production bio-molecular dynamics software specially optimized to run on graphics processing units (GPUs) on NVIDIA graphics cards. It reads CHARMM/NAMD and AMBER input files with a simple and powerful configuration interface. ACEMD allows performance equivalent to over 100 CPUs and microsecond long trajectories on workstation hardware.
ACEMD is the computational engine behind one of the largest distributed computing project worldwide GPUGRID.net nowdays summing thousands of GPUs. If you have a project for molecular simulations of excellent scientific quality which would benefit from running over GPUGRID, please contact us.
We are releasing licenses to collaborating groups on a discretionary basis. If you are doing world class research and you think that you can greatly benefit from ACEMD and GPUGRID, contact us. Otherwise, you can also independently get your fully licensed version for a fee at Acellera Ltd.
ACEMD is also available for professionals, and industries via Acellera Ltd. Download the ACEMD demo from Acellera Ltd.
ACEMD related publications:
M. J. Harvey and G. De Fabritiis, An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware, J. Chem. Theory Comput., 5, 2371–2377 (2009).pdf
*** M. Harvey, G. Giupponi and G. De Fabritiis, ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale, J. Chem. Theory and Comput. 5, 1632 (2009). pdf
G. Giupponi, M. Harvey and G. De Fabritiis, The impact of accelerator processors for high-throughput molecular modeling and simulation, Drug Discovery Today 13, 1052 (2008). pdf
Performance of ACEMD
ACEMD.gifACEMD performance compares to over 100 CPUs for DHFR.
DHFR, dihydrofolate reductase solvated in water, 23558 atoms, periodic boundary conditions, 9 A cutoff, PME long range electrostatic, hydrogen mass repartitioning, rigid bonds, Langevin thermostat, time step 4 fs
apoA1, 92,224 atoms, periodic boundary conditions, 9 A cutoff, PME long range electrostatic, hydrogen mass repartitioning, rigid bonds, Langevin thermostat, time step 4 fs
Villin headpieace, 13,701 atoms, periodic boundary conditions, 9 A cutoff, PME long range electrostatic, hydrogen mass repartitioning, rigid bonds, Langevin thermostat, time step 4 fs
Features of ACEMD
Input/output files compatibles with NAMD (pdb, psf, coor, parameter file, dcd, many configuration parameters)
Read Charmm force fields
Read Amber topology files
TCL scripting available for advanced jobs handling
Long time steps up to 4 fs (hydrogen mass repartitioning)
Rigid and harmonic hydrogen bonds
Particle mesh Ewalds (PME) long range electrostatics
Steered molecular dynamics simulations, umbrella sampling protocols
Metadynamics plugin for free energy calculations
Extensible plugin interface
Compatible with VMD and other visualization packages
Molecular structure creation via VMD or Amber tools
Manual pages and examples
Is there anything missing? Yes, just the barostat. At the moment, if you need to equilibrate the pressure for the first nanoseconds you can use any other code. All the production runs can be done then in NVT with ACEMD.
NVE.gifWe validate the code in several ways:
Energy conservation in the NVE ensemble and other validation tests.
ACEMD is run continuously by the gpugrid.net project thousands of times a day, every day of the year so that stability and robustness is one of the strongest point of the code.
We provide all the software support to report possible bugs by users. Finally, there is always the possibility of a mistake, in this case, we will try to fix it in the shortest time possible.