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From GROMACS to LAMMPS: GRO2LAM

A converter for molecular dynamics software
  • Hernán Chávez Thielemann
  • Annalisa Cardellini
  • Matteo Fasano
  • Luca Bergamasco
  • Matteo Alberghini
  • Gianmarco Ciorra
  • Eliodoro Chiavazzo
  • Pietro AsinariEmail author
Original Paper

Abstract

Atomistic simulations have progressively attracted attention in the study of physical-chemical properties of innovative nanomaterials. GROMACS and LAMMPS are currently the most widespread open-source software for molecular dynamics simulations thanks to their good flexibility, numerous functionalities and responsive community support. Nevertheless, the very different formats adopted for input and output files are limiting the possibility to transfer GROMACS simulations to LAMMPS. In this article, we present GRO2LAM, a modular and open-source Python 2.7 code for rapidly translating input files and parameters from GROMACS to LAMMPS format. The robustness of the tool has been assessed by comparing the simulation results obtained by GROMACS and LAMMPS, after the format conversion by GRO2LAM. Specifically, three nanoscale configurations of interest in both engineering and biomedical fields are studied, namely a carbon nanotube, an iron oxide nanoparticle, and a protein immersed in water. In perspective, GRO2LAM may be the first step to achieve a full interoperability between molecular dynamics software. This would allow to easily exploit their complementary potentialities and post-processing functionalities. Moreover, GRO2LAM could facilitate the cross-check of simulation results, guaranteeing the reproducibility of molecular dynamics models and testing their robustness.

Graphical Abstract

GRO2LAM, a modular and open-source Python code for rapidly translating input files and parameters from GROMACS to LAMMPS format

Keywords

Reproducibility Molecular dynamics GROMACS LAMMPS Conversion 

Notes

Acknowledgments

The authors acknowledge the high-performance computing initiative at Politecnico di Torino (HPC@Polito) and the CINECA Iscra C projects MISURPAC (HP10CJOR5E) and NANOCLUS (HP10CYC6UC) for the availability of high-performance computing resources and support. The authors would also like to acknowledge Dr. Rajat Srivastava for his useful suggestions. The authors declare no competing financial interests.

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of EnergyPolitecnico di TorinoTorinoItaly

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