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.