2. Quick Start

Given a PDB file 1iee.pdb, set up and run a simple simulation (assuming you have all other input files at hand such as the MDP files).

Start with importing the package. If you can find Gromacs in your shell then GromacsWrapper can find it, too. Check the release of the loaded Gromacs package:

>>> import gromacs
>>> print(gromacs.release())
2018.2

You can get help through the usual Python mechanisms:

>>> help(gromacs.pdb2gmx)
DESCRIPTION

gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files,
adds hydrogens to the molecules and generates coordinates in GROMACS
...
...
OPTIONS

Options to specify input files:

-f      [<.gro/.g96/...>]  (eiwit.pdb)
          Structure file: gro g96 pdb brk ent esp tpr
...
...

Now set up the system: (1) generate topology, (2) put in a dodecahedral simulation box, (3) solvate with water (for simplicity, we leave out the “add ions step”):

>>> gromacs.pdb2gmx(f="1iee.pdb", o="protein.gro", p="topol.top",
...                 ff="oplsaa", water="tip4p")
>>> gromacs.editconf(f="protein.gro", o="boxed.gro",
...                  bt="dodecahedron", d=1.5, princ=True,
...                  input="Protein")
>>> gromacs.solvate(cp="boxed.gro", cs="tip4p", p="topol.top",
...                 o="solvated.gro")

Given an MDP input file for energy minimization, generate the TPR file and run the energy minimization locally:

>>> gromacs.grompp(f="emin.mdp", c="solvated.gro", p="topol.top",
...                o="emin.tpr")
>>> gromacs.mdrun(v=True, deffnm="emin")

Assuming it all went well, set up and run a MD simulation, starting from the energy minimized system:

>>> gromacs.grompp(f="md.mdp", c="emin.gro", p="topol.top", o="md.tpr")
>>> gromacs.mdrun(v=True, deffnm="md")