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eSBMTools

eSBMTools is a python package that assists setup and evaluation of structure-based model (SBM) simulations of proteins and nucleic acids, both at Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard SBM.

eSBMTools is a powerful package that makes the job of running simulations much easier. It can generate the necessary files for running  simulations with GROMACS, compile data from several simulations, produce free energy graphs, make histograms and a lot more. Above all, it is designed to be simple to use and understand for the user.

The tools are well documented so that you can write your own python scripts for more complex problems and a better control over the simulation. To help you get a feel of what eSBMTools can do and its capabilities, a few examples have been compiled and are available in the package itself.

Free WHAM
Complex Formation
Contact Map Visualization
Q Histogram
Cα model