What it does
This tool performs a molecular dynamics simulation with GROMACS.
Input
- GRO structure file.
- Topology (TOP) file.
- A variety of other options can also be specified:
- MDP parameter file to take advantage of all GROMACS features. Otherwise, choose parameters through the Galaxy interface. See the manual for more information on the options.
- Accepting and producing checkpoint (CPT) input/output files, which allows sequential MD simulations, e.g. when performing NVT and NPT equilibration followed by a production simulation.
- Position restraint (ITP) file, useful for equilibrating solvent around a protein.
- Choice of ensemble: NVT or NPT.
- Whether to return trajectory (XTC or TRR) and/or structure (GRO or PDB) files.
Output
- Structure and/or trajectory files as specified in the input.