|Description||Molecular dynamics simulations of biological molecules.|
|Computational requirements||Programming language: C++
Dependencies: FFTW, cmake, CUDA
Memory requirements: Approximately 900 bytes memory use per atom in your system (typical systems have 10s of thousands and use Mbs of memory).
Disk requirements: Parallel I/O is not a strict requirement, but important for large runs.
Complementary tools: BAC.
|Type of software licence|
|Input requirements||Format: PDB (processed to provide .gro file and topology) and text configuration file.
Coming from: PDB can come from may sources (often the Protein Data Bank itself)
|Output requirements||Format: Variety of ASCII and binary formats (http://manual.gromacs.org/online/files.html) – standard = trr and xtc proprietary binary formats.
Used by: Tools provided in package and a wide range of molecular visualization and analysis packages (including VMD, MDAnalysis, etc.)
|Performance and HPC profile|
|Parallelism||Type of parallelism: MPI/GPU
Scalability: Typical run: 64 cores/1 GPU. Large run: 1024 cores/7 GPUs .
|Mode of operation||Multiple independent runs, one per scenario.|
|Deployed on||Frequently installed centrally on HPC resources (for example SuperMUC, Cartesius, Archer).|
|Benchmarks and examples||Benchmarks: http://www.palabos.org/academia/usecases
|Instructions for running on dedicated platforms|