Domain Molecular
Description Suite of molecular dynamics simulation, model building and analysis codes focussed on biological molecules.
User’s guide
Scientific articles
Computational requirements Programming language: C, C++, Fortran, and Python.
Memory requirements: Various (not high).
Disk requirements: Various (not high).
Complementary tools:BAC
Type of software licence GPL
Input requirements Format: Amber coordinates, DCD files, PDBs, Amber topology files, text configuration files.
Coming from: Amber (sander), NAMD, CHARMM.
Disk use: Depends on initial simulation.
Output requirements Format: Text or Amber Coordinate files, PDB files.
Used by:
Disk use: Typically kb and frequently of the order of hundreds.
Performance and HPC profile
Parallelism Type of parallelism: MPI
Scalability: Typical run: 1 core. Large run: 100 cores.
Mode of operation Usually batch analysis of frames from other MD codes (although sander, the Amber MD engine, is now included)
Deployed on SuperMUC, Archer
Getting started
Benchmarks and examples
Instructions for running on dedicated platforms