Simulations
Protocols for State-of-the-art Molecular Dynamics Simulations
Simulate Biological Systems with Best-in-Class Tools
Biomolecular processes rely on a variety of dynamic interactions between proteins, ligands, solvents and ions. Often, the specifics of these interactions are difficult to capture via physical experimentation alone due to the short time scales over which they occur. Simulation can help elucidate the energetics of these processes, providing insight into their mechanism of action and properties.
BIOVIA Discovery Studio utilizes best in-class molecular simulation programs, NAMD and CHARMm. Furthermore, Gaussian accelerated Molecular Dynamics (GaMD) is also implemented in the latest release of Discovery Studio for simultaneous unconstrained enhanced sampling and free energy calculations.
- Simulate
- Model
- Explore
Simulate
- CHARMm
- NAMD
- Perform explicit solvent MD simulations
- Solvate a protein with explicit membrane and run MD simulations
- DMol3 / CHARMm
- Calculate single point energies or perform minimizations of receptor-ligand complexes using hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) simulations
- Implementation of GaMD for simultaneous unconstrained enhanced sampling and free energy calculations
- Configure and run a GaMD equilibration, automatically parametrizing the boost potentials needed
- Run and restart GaMD simulations
- Estimate a free energy landscape from a set of MD trajectories, allowing for statistical reweighting of GaMD simulations
Model
- Support for a broad range of force fields, including CGenFF, charmm36, CHARMm and more
- MATCH method for typing ligands with charmm36
- Full support of CHARMM patching mechanism
- Fast explicit aqueous solvation method with optional counter-ions suitable for very large molecular systems
- Solvation of transmembrane protein into pre-equilibrated lipid bilayer
- Analysis of MD trajectories
Explore
- Perform quick and accurate protein ionization and residue pKs predictions for protein preparation
- Use CDOCKER, a CHARMm-based docking engine to perform flexible ligand-based docking and refinement
- Perform pose optimization of multiple ligands in the context of a receptor
- Calculate binding energies of docked poses
- Accurately predict relative ligand binding energy for a congeneric ligand series using the free energy perturbation (FEP) method
- Calculate the relative free energy of binding for a combinatorial library of ligands modeled by Multi-Site Lambda Dynamics (MSLD)
- Estimate ligand binding free energy and study ligand unbinding using CHARMm-based Steered Molecular Dynamics (SMD) simulations
- Examine electrostatic potential effects with CHARMm Poisson-Boltzmann (PB) equation
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FAQ About Molecular Dynamics Software & Programs
A molecular dynamics (MD) simulation is a computer-based method used to study the physical movements of atoms and molecules over time. It helps in understanding the behavior of complex systems by simulating atomic-level interactions under given conditions.
To be more precise, the molecular dynamics (MD) method of simulation is a computational technique used to model the physical movements of atoms and molecules over time. It simulates the interactions between particles (such as atoms, molecules, or ions) based on classical mechanics, typically using Newton's laws of motion. By calculating the forces between these particles, MD simulations predict how their positions evolve over time, allowing researchers to study the dynamic behavior of complex molecular systems like proteins, nucleic acids, or materials in different environments.
Molecular dynamics simulations provide insights into how drugs interact with their target proteins at the atomic level. This allows researchers to predict binding affinities, optimize drug candidates, and design more effective therapies without the need for extensive physical experimentation.
MD simulations help researchers visualize drug-target interactions, predict the stability of drug binding, and evaluate how molecular changes impact a drug's efficacy. This accelerates the identification of potential drug candidates and reduces the time and cost of experimental trials.
There are several types of MD simulations, including:
- classical MD (standard simulation of molecular systems),
- accelerated MD (for faster sampling of conformations),
- quantum mechanics/molecular mechanics (QM/MM) (hybrid simulations for chemical reactions),
- Gaussian accelerated MD (GaMD), which enhances sampling for complex biomolecular systems.
Here is a comparative table highlighting the key differences between NAMD and CHARMm in classical molecular dynamics simulations, covering aspects such as functionality, computational efficiency, system size, and use cases:
| Feature | NAMD | CHARMm |
|---|---|---|
| Primary Function | Specialized in parallel molecular dynamics simulations for large systems. | Molecular dynamics simulation software focused on force field calculations. |
| Developer | Developed by the Theoretical and Computational Biophysics Group (TCBG). | Developed by Accelrys/BIOVIA. |
| Computational Efficiency | Highly optimized for parallel processing on clusters and supercomputers. | Efficient for smaller systems; less focus on large-scale parallelization. |
| Force Fields Supported | Primarily uses CHARMM force fields but supports AMBER (biomolecular simulation program) and others. | Based on the CHARMM (Chemistry at Harvard Molecular Mechanics) force field. |
| System Size | Suitable for large biomolecular systems, such as proteins and membranes. | Ideal for smaller systems and QM/MM simulations. |
| GPU Support | Extensive GPU support for acceleration using CUDA. | Limited GPU acceleration via DOMDEC and OpenMM. |
| Advanced Features | Supports advanced simulations like steered MD, replica exchange MD. | Strong support for QM/MM simulations and ligand docking. |
| Use Cases | Best for large-scale, high-performance simulations of proteins and membranes. | Used for drug design, ligand docking, and detailed force field analysis. |
| Ease of Use | Requires some setup complexity for parallel computing. | Easier to set up for smaller systems or when integrated into Discovery Studio. |
| Community Support | Widely used in academic research with large user community. | More niche, used often in industry for drug discovery. |
Molecular dynamics simulations with BIOVIA Discovery Studio provide powerful tools like NAMD and CHARMm for accurately modeling complex biomolecular interactions. With Gaussian accelerated MD (GaMD) for enhanced sampling and free energy calculations, researchers can efficiently explore molecular processes. The software supports various force fields and molecular modeling techniques, making it essential for drug discovery, helping users simulate, model, and analyze interactions at an atomic level.
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