GROMACS is a versatile simulator to perform molecular dynamics simulations. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers and fluid dynamics.

A single simulation of GROMACS via Inductiva API can comprise several steps - e.g., preparing the molecules, minimizing the energy of the system, running the simulation and post-processing. Hence, to configure a simulation of GROMACS the user may require several files. Moreover, GROMACS has specific commands to run certain tasks that already use the files in your input directory.


This example runs a simple case of the molecular dynamics of water molecules inside a small box.

import inductiva

input_dir = inductiva.utils.download_from_url(
    "", unzip=True)

commands = [
    "gmx solvate -cs tip4p -box 2.3 -o conf.gro -p",
    "gmx grompp -f energy_minimization.mdp -o min.tpr -pp -po min.mdp -c conf.gro -p",
    "gmx mdrun -s min.tpr -o min.trr -c min.gro -e min.edr -g min.log",
    "gmx grompp -f positions_decorrelation.mdp -o decorr.tpr -pp -po decorr.mdp -c min.gro",
    "gmx mdrun -s decorr.tpr -o decorr.trr -x  -c decorr.gro -e decorr.edr -g decorr.log",
    "gmx grompp -f simulation.mdp -o eql.tpr -pp -po eql.mdp -c decorr.gro",
    "gmx mdrun -s eql.tpr -o eql.trr -x trajectory.xtc -c eql.gro -e eql.edr -g eql.log",

gromacs = inductiva.simulators.GROMACS()

task =,