From GROMACS to LAMMPS: GRO2LAM : A converter for molecular dynamics software

Area of Science:

• Computational chemistry and materials science.
• Nanotechnology and advanced materials.
• Biophysics and computational biology.

Background:

• Atomistic simulations are crucial for understanding nanomaterial properties.
• GROMACS and LAMMPS are leading open-source molecular dynamics software.
• Incompatible file formats hinder seamless simulation workflow transfer between GROMACS and LAMMPS.

Purpose of the Study:

• To develop a tool for translating GROMACS input files to LAMMPS format.
• To enable easier data exchange and utilization of complementary features between GROMACS and LAMMPS.
• To enhance reproducibility and cross-checking of molecular dynamics simulations.

Main Methods:

• Development of GRO2LAM, a modular, open-source Python 2.7 code.
• Translation of input files and parameters from GROMACS to LAMMPS format.
• Validation through comparative simulations of carbon nanotubes, iron oxide nanoparticles, and proteins in water.

Main Results:

• GRO2LAM successfully translates GROMACS input files and parameters to LAMMPS format.
• Comparative simulations demonstrate the robustness of the conversion process.
• The tool facilitates the study of diverse nanoscale systems, including those relevant to engineering and biomedicine.

Conclusions:

• GRO2LAM enhances interoperability between GROMACS and LAMMPS molecular dynamics software.
• The tool supports the exploitation of complementary functionalities and post-processing capabilities.
• GRO2LAM aids in cross-validating simulation results and ensuring model robustness and reproducibility.