Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory [Article v1.0].

Area of Science:

• Computational chemistry
• Molecular dynamics simulations

Background:

• Grid Inhomogeneous Solvation Theory (GIST) offers detailed solvation analyses.
• GIST provides high spatial resolution and energy/entropy decomposition.
• GIST has a steep learning curve for new users.

Purpose of the Study:

• To provide a tutorial for GIST analysis.
• To simplify common GIST analysis steps.
• To guide users through practical aspects of GIST.

Main Methods:

• Utilizing molecular dynamics (MD) simulations.
• Applying Grid Inhomogeneous Solvation Theory (GIST).
• Using Jupyter notebooks and the gisttools Python package.

Main Results:

• Demonstration of GIST analysis using the streptavidin-biotin complex.
• Simplified workflow for GIST analysis.
• Discussion of GIST theory with practical considerations.

Conclusions:

• The tutorial and provided tools lower the barrier to entry for GIST analysis.
• Users can perform detailed solvation free energy calculations more easily.
• The study facilitates deeper understanding of solvation phenomena.