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
Instructions for running on dedicated platforms