Gromacs (1)
Summary
Contact http://www.gromacs.org
Domain Molecular.
Description Molecular dynamics simulations of biological molecules.
Documentation
User’s guide
Scientific articles
Requirements
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.)
Disk use:
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).
Getting started
Benchmarks and examples Benchmarks: http://www.palabos.org/academia/usecases
Examples: http://www.palabos.org/documentation-quick
Instructions for running on dedicated platforms