GROMACS molecule & liquid database.

Area of Science:

• Computational chemistry
• Molecular dynamics simulations
• Physical chemistry

Background:

• GROMACS is a widely used, efficient, and accessible molecular dynamics simulation package.
• Validating simulations requires comparing results with experimental data.
• A web-based database simplifies setting up simulations and provides pre-calculated properties.

Purpose of the Study:

• To create a database of simulated liquid properties for organic molecules.
• To facilitate the validation of molecular dynamics simulations.
• To provide readily accessible simulation data and experimental comparisons.

Main Methods:

• Simulated liquid properties for 145 organic molecules using GROMACS.
• Employed two distinct molecular dynamics force fields: OPLS all atom and Generalized Amber Force Field.
• Calculated eight key liquid properties: density, enthalpy of vaporization, surface tension, heat capacity (constant volume and pressure), isothermal compressibility, volumetric expansion coefficient, and static dielectric constant.

Main Results:

• Generated simulated liquid properties for 145 organic molecules across two force fields.
• Compiled data for eight physical properties, including density and surface tension.
• Database includes simulated structures, topologies, and experimental values for comparison.

Conclusions:

• The database provides valuable data for validating molecular dynamics simulations.
• It serves as a resource for researchers in physics, chemistry, and biology.
• The database is freely available at http://virtualchemistry.org.