Molecular Dynamics (MD) simulation codes are specialized computer programs used in the field of computational chemistry and physics to study the dynamic behaviour of atoms and molecules over time. These codes employ numerical algorithms to solve Newton's equations of motion for each particle in a molecular system, allowing researchers to simulate the motion and interactions of atoms and molecules at the atomic or molecular level. MD simulation codes play a crucial role in understanding the behaviour of matter at the microscopic scale, providing insights into various physical and chemical processes. They are widely used in fields like materials science, biophysics, and chemistry to investigate phenomena such as protein folding, chemical reactions, phase transitions, and more.
The functionalities of MD simulation codes are diverse and powerful. They enable scientists to model and analyze the thermal, structural, and dynamical properties of molecular systems under different conditions, such as temperature, pressure, and external forces. These codes can provide information about the trajectory, energy, and thermodynamic properties of a system, allowing researchers to observe how molecules move, interact, and change over time. By manipulating parameters and initial conditions, researchers can investigate a wide range of scientific questions, predict material properties, and design novel molecules or materials with desired characteristics. MD simulation codes also offer the ability to test theoretical models and validate experimental observations, making them an indispensable tool in the study of molecular behaviour.
In CompBioMed we make use of different MD codes, in particular in the field of drug discovery with applications such as the Binding Affinity Calculator (BAC) or PlayMolecule, which can use different backend MD applications.