We present a software for practical interaction energy based analysis of protein molecular simulation trajectories:

Onur Serçinoğlu, Pemra Ozbek; gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations, Nucleic Acids Research, , gky381, https://doi.org/10.1093/nar/gky381

Main functionality includes:

• Calculation of pairwise amino acid non-bonded interaction energies from NAMD or GROMACS generated Molecular Dynamics (MD) simulation trajectories by interoperating with NAMD/GMX simulation engines.
• Equal-time linear correlations between interaction energy time series.
• Custom residue selections & multiple processor usage.
• A visualization interface for:
• Viewing pairwise interaction energies and their correlations alongside an embedded PyMol molecular viewer.
• Protein Energy Network construction and visualization of simple residue-based local network metrics (Degrees, Betweenness Centrality and Closeness Centrality)
• Shortest path analysis

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