OpenMM2gmx

A workflow for converting and centering OpenMM trajectories using GROMACS. Works for any system and has been tested on membrane proteins with a triclinic box.

Overview

This repository provides a workflow to:

• Generate .gro , .top and .tpr files from OpenMM outputs
• Convert OpenMM .dcd trajectories into GROMACS-compatible .xtc , handling esapcially difference between triclinic box definiton between openmm and gromcas
• treating the the trajectory with no jump and center options around a selection of residues (eg. Center of mass of the protein)

Authors

• Alaa REGUEI, PhD Student - Université Paris Cité, BFA.
• Samuel Murail, Associate Professor - Université Paris Cité, BFA.

Installation

You will need first to install parmed and openmm ,we recommend using conda ;

Make sure you have GROMACS installed and available in your PATH (e.g. gmx trjconv, gmx make_ndx). To install it , please refer to official guide : https://manual.gromacs.org/current/install-guide/index.html

git clone https://github.com/regueialaa/OpenMM2gmx.git
cd OpenMM2gmx
pip install .
OpenMM2gmx --help

Usage

OpenMM2gmx can be used either from the command line or directly in Python (e.g., in a Jupyter Notebook).

Option 1: Command line

Run the script with the following arguments:

OpenMM2gmx \
  --top topfile.parm7 \
  --xml system.xml \
  --traj traj1.dcd traj2.dcd \
  --mdp simulation.mdp \
  --center_res COM \
  --sim_name my_simulation \
  --stride 1 \
  --save_mode 0 \
  --output_dir MD_output

Option 2: Python / Jupyter Notebook

OpenMM2gmx can also be imported and used directly in Python scripts or Jupyter Notebooks.

An example notebook demonstrating the package on a Class B GPCR system is provided:

GPCR_case.ipynb

This tutorial shows how to import the package and run the workflow directly from a Python environment.

Arguments

--top (required) Input topology file : eg. parm7 (recommanded for membrane systems) , pdb , cif or mmcif

--xml (required) OpenMM coordinates/system XML file from the production run

--traj (required) One or more OpenMM trajectory files (e.g. traj.dcd or traj_part1.dcd traj_part2.dcd ...). You can pass multiple files.

--mdp (required) Input GROMACS .mdp file

--center_res (required) Residue used to define the simulation center: "COM" centers on the residue closest to the center of mass of the system, or you can specify your own residue in the form "resid100". Example: --center_res "COM" (default) or --center_res "resid:A:100"'

--sim_name (required) Name of the simulation/replica (used in output filenames and logs)

--stride (optional) Stride for trajectory analysis (default: 1).

--save_mode (optional) Output mode (default: 0). 0 = full corrected system trajectory (Protein + non-polymer), 1 = protein-only corrected trajectory, 2 = both trajectories

--output_dir (optional) Output directory name (default: MD_output)

References

If you use OpenMM2gmx in your work, please cite the following software packages:

• OpenMM: Eastman et al. (2024). OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The Journal of Physical Chemistry B, 128 (1), 109–116.

• GROMACS: Abraham et al. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25.