GROMACS

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.

Example

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(
    "https://storage.googleapis.com/inductiva-api-demo-files/"
    "gromacs-input-example.zip", unzip=True)

commands = [
    "gmx solvate -cs tip4p -box 2.3 -o conf.gro -p topol.top",
    "gmx grompp -f energy_minimization.mdp -o min.tpr -pp min.top -po min.mdp -c conf.gro -p topol.top",
    "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 decorr.top -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 eql.top -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 = gromacs.run(input_dir=input_dir,
                   commands=commands)

task.wait()
task.download_outputs()