Overview

MartiniSurf builds complete GROMACS-ready systems for:

  • Protein-surface workflows (Martini 3)

  • DNA-surface workflows (Martini2 DNA)

  • Linker and non-linker orientation workflows

  • Pre-CG complex workflows (--complex-config)

Main capabilities

  • Coarse graining with martinize2 (protein) and martinize-dna.py (DNA)

  • Generated or user-provided surfaces

  • Orientation by residue anchors (Not explicit Linker mode)

  • Explicit linker mode

  • Automatic topology assembly

  • Optional solvation, ionization, and DNA water freezing

Output structure

Typical output folder:

Simulation_Files/
  0_topology/
  1_mdp/
  2_system/