Software projects: Gromacs (2)

Gromacs (2)
Domain Biomedical research
Description Standard Molecular Dynamics (MD) to calculate Residence Times and Binding affinities.

For the MD (Gromacs) calculation will be looking at running 3 calculations to covering the M3 Muscarinic receptor and 2 Adenosine Receptors. These will contain approximately 15,000 atoms and we will have expected simulation times of several milliseconds.

We are likely to want to run these calculations on GPU’s and we expect them to take 1 or 2 weeks of GPU time dependent on the GPU available.

User’s guide
Scientific articles
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:
Complementary tools:
Type of software licence  LGPL
Input requirements Format: GROMACS input pdb + Ligand.
Coming from: Prepared at Evotec.
Disk use: 3 input files for 3 GPRCs.
Output requirements Format: Variety of ASCII and binary formats ( – 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: 3 output files for 3 GPRCs.
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 Will be run on a single or multiple GPU depending on what is available at HPC centre.
Deployed on Frequently installed centrally on HPC resources (for example SuperMUC, Cartesius, Archer).
Getting started
Benchmarks and examples
Instructions for running on dedicated platforms