Steered Molecular Dynamics (SMD) simulates atomic force microscopy (AFM) experiments and is particularly useful for studying processes such as protein folding, protein-ligand binding, and the mechanical properties of biomolecules.
Alfa Chemistry combines expertise in molecular dynamics simulations, bioinformatics and computational chemistry to provide customized SMD simulation solutions based on your specific research or development needs.
Whether you're in drug discovery, materials science or protein engineering, our SMD simulation services can help you accelerate projects and drive innovation.
Learn About SMD
SMD is an enhanced sampling method used to explore force and free energy distribution along selected directions. In SMD simulations, additional external forces are applied to one or more atoms to induce specific conformational changes or to probe the mechanical response of the system.
SMD simulations are often combined with other computational techniques, such as free energy calculations or enhanced sampling methods, to obtain more accurate and reliable results.
Figure 1. Steered molecular dynamics (SMD). A continuous external force is used to pull the ligand out of the target protein binding site along the reaction coordinate ('collective variable', CV). (Salo-Ahen O, et al. 2020)
Application of Our SMD Simulations
- Understanding protein-ligand interactions: SMD simulations can provide valuable information on binding affinities, binding pathways, and conformational changes, facilitating rational drug design and accelerating the discovery of new compounds.
- Revealing protein dynamics and folding: By applying controlled forces, SMD simulations can probe the mechanical properties of a protein, reveal its stability, and help understand mutations associated with the disease.
- Engineered biomaterials: By subjecting biomolecules to external forces, SMD simulations can predict mechanical properties, study material deformation, and guide the design of innovative materials with customized functionality.
- Improve the efficiency of chemical process design: By simulating the behavior of molecules under the influence of external forces, you can gain insights into reaction mechanisms, transition states, and energy landscapes.
- Enhanced material characterization: By subjecting materials to controlled forces, SMD simulations can elucidate mechanical properties, study material response to stress, and predict material failure mechanisms.
SMD Simulation Tools
Alfa Chemistry generally uses the following software tools for SMD simulation services.
Our SMD Simulation Process
1. System Preparation
Starting structures are usually obtained from experimental data or generated using molecular modeling tools. The system is then solvated in an appropriate solvent environment and, if necessary, neutralized by adding counterions.
2. Force Field Selection
Force fields are chosen to describe the interactions between atoms in the system. Commonly used force fields include AMBER, CHARMM, GROMOS, etc.
3. System Energy Minimization
This step helps relieve any stress or deformation in the system.
4. System Equilibration
Two equilibrium stages are typically performed: NVT (constant number of particles, volume, and temperature) and NPT (constant number of particles, pressure, and temperature) ensembles.
5. Production Simulations
The core of SMD simulation involves applying external forces to the system. These forces can be applied in a variety of ways, depending on the goals of the simulation.
The equations of motion are solved numerically to simulate the dynamics of the system over time, taking into account the potential energy generated by the force field and the applied external forces.
6. Data Analysis
The generated trajectories are analyzed to extract meaningful insights. We employ a variety of analytical techniques, including calculating structural properties, monitoring conformational changes, analyzing energy landscapes, and studying mechanical properties.
7. Interpretation and Validation
We interpret simulation results and validate them against experimental data or theoretical expectations.
Contact us today to discuss your specific needs and discover how our SMD simulation services can accelerate your research, enhance innovation, and drive progress in your industry.
- Salo-Ahen O, et al. (2020). "Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development." Processes, 9(1), 711.