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AceMD a software for high-throughput molecular dynamics
- AceMD is a bio-molecular dynamics software specially optimized to run on graphics processing units (GPUs) on NVIDIA graphics cards. acemd is designed to be a specialized fast production MD engine for GPU devices to be used for high-throughput molecular dynamics production runs.
AceMD is the computational engine behind the distributed computing project gpugrid.net. AceMD is available for professionals, and industries via the company Acellera Ltd. For academic users the fully licensed version is available at a discounted rate in order to contribute to code development and support costs.
Features of aceMD
- Input/output files compatibles with NAMD (pdb, psf, coor, parameter file, dcd, many configuration parameters)
- Read Charmm force fields and Amber in Charmm format
- Read coarse-grained force fields (coming soon)
- TCL scripting available for advanced jobs handling
- Long time steps up to 4 fs (hydrogen mass repartitioning)
- Rigid and harmonic hydrogen bonds
- Langevin thermostatting
- Generalized reaction field for long range electrostatics
- Steered molecular dynamics simulations
- Compatible with VMD and other visualization packages
- Example simulations with inputs and molecular structures
- Molecular structure creation via VMD/NAMD
- A forum for users
- Effective manual pages
Performance of aceMD
- Dihydrofolate reductase solvated in water, 23558 atoms, periodic boundary conditions, 12 A cutoff, generalized reaction field long range electrostatic, heavy hydrogens, rigid bonds, time step 4 fs
- 28 ns/day on 2 NVIDIA Geforce 9800 GX2, 4 GPU cores. (12 ms/step)
- 7.6 ns/day on 1 core of NVIDIA Geforce 9800 GX2. (45 ms/step)
- 6.2 ns/day on NVIDIA Geforce 8800GT. (55 ms/step)
The PC used for these benchmark is based on a NVIDIA 780i motherboard, 4GB RAM, Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz an 3 Nvidia Geforce 9800 GX2 running Linux Fedora 8 and NVIDIA CUDA SDK 1.1.
Manual Pages
Manual pages are provided for aceMD with input commands, ways of use, examples and so on. These pages assume that you have familiarity with molecular dynamics simulations (a list of suggested references is also available in the manual). Go to the manual pages.
Code Validation
We validate the code in several ways:
- We execute a set of validation tests for which we check the energy of the first configuration against standard molecular dynamics packages. All these tests are performed when a new release is produced.
acemd is run continuously by the gpugrid.net project hundred 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 a forum where possible bugs can be reported by any user and which you can consult to find possible solutions and help. Finally, there is always the possibility of a mistake, in this case, we will try to fix it in the shortest time possible thanks to the resources coming from the subscription fee.
Download
Download of the software requires a simple quick registration via this web site (coming soon).