Lipids play a crucial role in the structure and function of cell membranes. Membrane simulation intend to probe molecular level interactions between single molecules and provide complementary information to experiments. Lipid membrane simulations software tools are used to setup, perform, and analyze molecular dynamics simulations.
Allows molecular simulation. CHARMM is a program that focuses on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. The software offers a set of energy functions and several sampling methods. It has applications for many-particle systems, as well as for inorganic materials, with applications in materials design.
Provides numerous programs that work together to setup, perform, and analyze molecular dynamics (MD) simulations. AMBER is a biomolecular simulation package which also contains software designed to parameterize more complex molecules and fragments not currently present in the force field libraries. The suite can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
Performs atom typing and assignment of parameters and charges by analogy in a fully automated fashion. The CGenFF atom typer uses a programmable decision tree. Assignment of bonded parameters is based on substituting atom types in the definition of the desired parameter and charges are assigned using an extended bond-charge increment scheme that can capture short- and medium-range inductive and mesomeric effects.
Allows the modeling of ring structures, with an application to cholesterol. MARTINI is a program designed for performing biomolecular simulations. The key feature of its model is its systematic parametrization based on thermodynamic data, especially experimental partitioning data.
Helps user to generate a series of CHARMM inputs necessary to build a protein/membrane complex for molecular dynamics simulations. CHARMM-GUI Membrane Builder helps a wide range of scientists who simulate complex lipid membranes, both with and without peptides and proteins. It assists user in production of ligand force field (FF) parameter, structure, and other necessary files for various ligand-containing biomolecular simulations.
Provides a high-performance of molecular dynamics simulations. Desmond includes protein-ligand complexes, small molecules in mixed solvents, organic solids, and synthetic macromolecular complexes. This tool excels in numerical accuracy, which helps to ensure proper modelling of certain thermodynamic relationships that depend on detailed balance. In addition, Desmond provides a robust framework for the calculation of energies and forces for various force field models and is compatible with those models commonly used in both biomolecular and condensed-matter research.