ArticleJournal of molecular modeling2019
From GROMACS to LAMMPS: GRO2LAM : A converter for molecular dynamics software.
Article in Journal of molecular modeling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Ultrastructural Changes in Final Instar Larvae ofBiomimetics (Basel, Switzerland) · 2025Article
- Calceolarioside B inhibits SARS-CoV-2 Omicron BA.2 variant cell entry and modulates immune response.Virology journal · 2024Article
- Shale Gas Nanofluid in the Curved Carbon Nanotube: A Molecular Dynamics Simulation Study.ACS omega · 2024Article
- Boundary Lubrication Performance of Polyelectrolyte-Surfactant Complexes on Biomimetic Surfaces.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Computational Insights into Captopril's Inhibitory Potential Against MMP9 and LCN2 in Bladder Cancer: Implications for Therapeutic Application.Cancer informatics · 2024Article
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- Computational insight into stability-enhanced systems of anthocyanin with protein/peptide.Food chemistry. Molecular sciences · 2023Article
- PyL3dMD: Python LAMMPS 3D molecular descriptors package.Journal of cheminformatics · 2023Article
- Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry.Membranes · 2023Review
- Revisiting the Proposition of Binding Pockets and Bioactive Poses for GSK-3β Allosteric Modulators Addressed to Neurodegenerative Diseases.International journal of molecular sciences · 2021Article
- In Vitro and In Silico Anti-Arboviral Activities of Dihalogenated Phenolic Derivates of L-Tyrosine.Molecules (Basel, Switzerland) · 2021Article
- Computational molecular docking and virtual screening revealed promising SARS-CoV-2 drugs.Precision clinical medicine · 2021Review
- Mechanistic correlation between water infiltration and framework hydrophilicity in MFI zeolites.Scientific reports · 2019Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.