Domain Molecular
Description Molecular dynamics simulations of biological molecules.
User’s guide
Scientific articles
Computational requirements Programming language: C and C++
Dependencies: FFTW (& TCL for scripting)
Memory requirements: Approximately 3 kb memory use per atom in your system (typical systems have 10s of thousands and use Mb to hundreds of Mb of memory)
Disk requirements:
Complementary tools: BAC
Type of software licence Bespoke – Free for non-commercial use (requires registration)
Input requirements Format: PDB and topology/parameters. Typically XPLOR PSF and CHARMM parameter file or Amber prmtop file.
Coming from: PDB can come from may sources (often the Protein Data Bank itself). Processed PDB from CHARMM, VMD or AmberTools.
Disk use:
Output requirements Format: DCD
Used by: 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 Flexible . many applications use single extreme parallel run but increasingly multiple parallel runs used to gain efficient sampling. Multiple runs may also run concurrently and communicate (for example in replica exchange simulations).
Deployed on Frequently installed centrally on HPC resources (for example SuperMUC, Cartesius, Archer)
Getting started
Benchmarks and examples
Instructions for running on dedicated platforms