MD Simulation

Our molecular dynamics simulation services provide detailed insights into the dynamic behavior and stability of biomolecules and their complexes. Using advanced software like GROMACS and AMBER, we simulate proteins, ligands, and nucleic acids in realistic environments with explicit solvent and appropriate force fields. These simulations help analyze conformational changes, binding interactions, and the impact of mutations over time, supporting drug design, protein engineering, and functional studies. Comprehensive analysis and clear reports are delivered to aid your research goals.

Molecular Dynamics (MD) Simulation Services –

• System Setup: Protein, ligand, or complex preparation with solvation and ionization.

• Simulation Engines: GROMACS for accurate simulations

• Solvation Models: Explicit/implicit water models (e.g., TIP3P, SPC) in defined box types.

• Force Fields: Use of industry-standard force fields (CHARMM, AMBER, OPLS-AA, etc.).

• Simulation Time: Ranging from nanoseconds to microseconds, based on project goals.

• Trajectory Analysis: RMSD, RMSF, Rg, hydrogen bonds, SASA, PCA, and clustering.

• Stability & Dynamics: Insight into conformational stability and interaction dynamics.

• Binding Behavior: Study of ligand stability, flexibility, and binding persistence.

• Deliverables: Trajectory files, plots, interaction data, and an interpretation report.

• Applications: Drug binding studies, mutation impact analysis, protein folding, and stability assessment.