SMOG

SMOG@ctbp is a web server that provides a simplified approach to implementing structure-based Hamiltonians on the GROMACS molecular dynamics package, enabling the study of large-scale motions in proteins and RNAs. This tool is especially useful for those unfamiliar with molecular dynamics, as it provides a tutorial-like format to help speed up the learning curve. Users can upload a multi-chain biomolecular system in PDB format and receive all the necessary files as output. Additionally, both C(alpha) and all-atom models are available.

Molecular dynamics simulations with coarse-grained and/or simplified Hamiltonians have been proven effective in capturing the functionally important long-time and large-length scale motions of proteins and RNAs. In recent years, structure-based Hamiltonians, which are simplified models developed from the energy landscape theory of protein folding, have become a standard tool for investigating biomolecular dynamics. SMOG@ctbp is an effort to simplify the implementation of structure-based models, which have proven to be a powerful tool in this area.

The first objective of the web tool is to simplify the process of implementing a well-characterized structure-based model on a state-of-the-art, open-source molecular dynamics package, GROMACS. The second objective is to provide a tutorial-like format that helps speed up the learning curve of those who are unfamiliar with molecular dynamics. By providing a user-friendly and accessible approach, SMOG@ctbp makes it possible for researchers to investigate biomolecular dynamics without requiring extensive knowledge of molecular dynamics.