STOCK: structure mapper and online coarse-graining kit for molecular simulations

Area of Science:

• Computational Chemistry
• Molecular Modeling
• Biophysics

Background:

• Coarse-grained (CG) molecular simulations offer a computationally efficient approach to study large molecular systems.
• Developing accurate CG models requires robust methods for structure mapping and effective potential generation.
• Existing methods can be complex and require specialized expertise, limiting accessibility.

Purpose of the Study:

• To present a user-friendly web toolkit for setting up coarse-grained molecular simulations.
• To provide tools for molecular structure mapping and effective potential generation.
• To facilitate the application of CG simulations across various research domains.

Main Methods:

• The toolkit comprises two primary tools: structure mapping and Boltzmann inversion.
• A graphical user interface (GUI) facilitates the definition of mappings from all-atom to CG resolutions.
• The Boltzmann inversion tool generates effective potentials by preserving structural properties, such as radial distribution functions.

Main Results:

• The structure mapping tool generates input files compatible with standard CG packages (e.g., VOWLS, DL_CGMAP).
• Effective potentials were successfully derived for TIP3P water and salt solutions.
• The toolkit's applicability was validated using pentane and polyalanine molecules.

Conclusions:

• The STructure mapper and Online Coarse-graining Kit (STOCK) provides an accessible platform for CG simulation setup.
• The toolkit simplifies the generation of CG models and effective potentials, enhancing research efficiency.
• STOCK is available online, promoting wider adoption and application in molecular simulations.