Recommended Examples¶

The recommended complete workflows are:

Protein + Not explicit Linker + solvate + ionize¶

Path: martinisurf/examples/protein/04_anchor_solvate_ionize

cd martinisurf/examples/protein/04_anchor_solvate_ionize
bash run.sh
bash work_flow_gromacs.sh

DNA + linker + solvate + ionize + frozen water¶

Path: martinisurf/examples/dna/03_linker_solvate_ionize_freeze

cd martinisurf/examples/dna/03_linker_solvate_ionize_freeze
bash run.sh
bash work_flow_gromacs.sh

Behavior notes:

In DNA linker mode, linker-DNA is coupled with bonded terms (bond + angle) in topology (no linker-DNA pull coordinate).
work_flow_gromacs.sh uses non-restrained topology in equilibration stages and restricted topology in production when available.

Pre-CG protein+cofactor + substrate + solvate + ionize¶

Path: martinisurf/examples/protein/05_pre_cg_nad_substrate

cd martinisurf/examples/protein/05_pre_cg_nad_substrate
bash run.sh
bash work_flow_gromacs.sh

Behavior notes:

In pre_cg_complex, low-Z balancing is enabled by default.
Default low-Z fraction is 0.2 unless protein.balance_low_z_fraction is provided in complex_config.yaml.

Protein build-only examples¶

martinisurf/examples/protein/01_anchor
martinisurf/examples/protein/02_adsorption
martinisurf/examples/protein/03_linker_surface_decoration

DNA build-only examples¶

martinisurf/examples/dna/01_anchor
martinisurf/examples/dna/02_linker

Surface-focused examples¶

martinisurf/examples/surfaces/01_protein_cnt_3d
martinisurf/examples/surfaces/02_protein_graphene_resizable
martinisurf/examples/surfaces/03_protein_bilayer_hexagonal

Adsorption mode note¶

For adsorption setups, use the main build command with --ads-mode and anchor-based orientation (--anchor ... or --complex-config anchor groups). This mode runs: minimization -> nvt -> npt -> production without deposition pulls/restraints.

For the current DNA linker workflow example (dna/03), the MD protocol is: minimization -> nvt -> deposition (NPT) -> production (NVT). There is no separate npt.mdp stage in this workflow; the pressure-coupled step is deposition.