Predict Motion, Not Just Structure — Molecular Dynamics Simulations at Atomic Resolution
Static models can't explain everything. At Creative Proteomics, we help you explore how biomolecules move, interact, and function—under realistic conditions and in dynamic detail.
Molecular Dynamics (MD) simulation is a physics-based computational method that models the motion of atoms and molecules over time. By numerically solving Newton's equations of motion at femtosecond time steps, MD reveals how biomolecules behave in explicit solvent environments under defined temperature, pressure, and ionic conditions.
Unlike static techniques such as X-ray crystallography or cryo-EM, MD simulations provide 4D insights—capturing conformational changes, transient interactions, and structural fluctuations that are essential for understanding biological function. Systems that can be modeled include:
With MD, we can go beyond structure—into motion, mechanism, and prediction.
MD simulations are uniquely suited to address biological problems where molecular motion, flexibility, or specificity is critical but experimentally inaccessible. Whether you are exploring basic mechanisms or pre-screening drug candidates, MD provides actionable insight into:
Molecular Functions
Research Problems Solved
These capabilities are often applied in structural refinement, virtual screening validation, mutation effect prediction, and transport mechanism studies. Creative Proteomics tailors every simulation to your scientific question, system complexity, and analysis depth—offering both clarity and confidence.
Model-Ready Flexibility — Sequence or Structure Supported
We simulate systems from crystal structures, homology models, or AlphaFold2 predictions—with loop modeling and accurate protonation adjustment.
Function-Focused Design — Beyond Stability Assessment
Our simulations capture conformational transitions, transient pocket dynamics, and induced-fit behavior critical to biomolecular function.
Native-Like Environments — Water, Ions, and Membranes Included
Simulations are performed under explicit solvent, physiological salt, and membrane embedding conditions, mimicking realistic biological environments.
Non-Standard System Support — Glycans, Metals, and Cofactors
We accommodate complex biomolecules including glycosylated proteins, metal coordination centers, and ligand-bound assemblies beyond standard topologies.
Hypothesis-Driven Configuration — Aligned with Your Research Goals
Each simulation is custom-built based on your research objective—such as mutation analysis, transport dynamics, or ligand residence time.
Atomistic Resolution — Visualize Motion Beyond Static Snapshots
Simulations run at femtosecond resolution, capturing dynamic events like binding/unbinding, domain motion, and allosteric transitions over time.
Binding Accuracy — Go Beyond Docking Scores
We refine ligand-target complexes via equilibrium MD and compute binding affinities (MM/PBSA, FEP) to improve predictive accuracy in flexible systems.
Recommended For: Small molecule optimization, structure-based drug design
Recommended For: Mechanism-of-action studies, enzyme design, mutant analysis
Recommended For: GPCRs, ion channels, ABC transporters, lipid-interacting enzymes
Recommended For: Antisense drug development, CRISPR studies, epigenetic research
Recommended For: Variant impact studies, disease mutation modeling, protein engineering
Recommended For: Formulation stability, solubility prediction, salt effect studies
Project Consultation & System Definition
Clarify research goals, target molecule, and simulation objectives. Choose appropriate force fields, solvent models, and simulation engines. Define analysis scope and reporting format.
Structure Preparation & Model Optimization
Clean PDB files, fix missing parts, assign protonation states, and optimize side chains. Perform homology modeling or loop refinement if needed. Parameterize non-standard residues or ligands.
System Construction & Solvation
Set simulation box size and shape. Add solvent, ions, and membranes if applicable. Neutralize charge and minimize energy to remove clashes.
Equilibration
Gradually heat system with restraints. Equilibrate temperature and pressure under NVT/NPT ensembles. Monitor stability and adjust if necessary.
Production Simulation
Run full MD trajectory over defined timescale, saving snapshots regularly. Use enhanced sampling if needed. Monitor and restart as required.
Post-Simulation Analysis
Analyze structural and energetic properties, perform clustering, PCA, and specific event tracking. Generate figures and animations if requested.
Reporting & Data Delivery
Provide raw trajectories, structure files, input scripts, and a comprehensive report. Offer data archiving and support if desired.
| Engine | Specialization |
| GROMACS | High-speed all-atom simulations, especially large systems |
| AMBER | Biomolecular force fields and free energy calculations |
| NAMD | Parallel efficiency for large-scale simulations |
| LAMMPS | Materials modeling and hybrid potential support |
| Desmond | High-throughput MD and drug discovery workflows |
Each engine is validated for consistency, performance, and compatibility with downstream tools.
We provide system-specific parameterization using well-established and customizable force fields:
We support parameter fitting for non-standard residues, cofactors, metal centers, and synthetic compounds using quantum-derived charges (RESP, AM1-BCC) when necessary.
Capturing Fast or Rare Conformational Events
Simulate hinge motions, loop transitions, and transient structural states to explore energy landscapes and dynamic equilibria.
Refining Incomplete or Flexible Structures
Extend partial models, rebuild missing regions, and assess local flexibility to improve fit with cryo-EM, NMR, or SAXS data.
Modeling Binding Dynamics and Hit Optimization
Validate docking poses, simulate ligand entry/exit, and assess induced fit for lead prioritization and binding mechanism studies.
Testing Design Flexibility and Structural Stability
Evaluate linker dynamics, domain motion, and overall construct behavior under physiological conditions before lab implementation.
Simulating Dynamic Antigen–Antibody Interactions
Reveal CDR flexibility, epitope accessibility, and interface breathing beyond static co-crystal data for rational immunogen design.
| Category | Details |
| Molecular Structure |
|
| Ligands & Non-Standard Molecules |
|
| System Conditions |
|
| Simulation Objective |
|
| Optional Experimental Data |
|
Trajectory Files
Receive full-length simulation trajectories (.xtc, .trr, or .dcd formats), suitable for playback, visualization, or further analysis.
Topology & Input Files
We deliver all system configuration files, including coordinate files, topology definitions (.top/.psf), and input scripts used in setup.
Energy & Log Files
Simulation energy profiles, pressure, temperature, and performance metrics are included to validate simulation stability and reproducibility.
Analysis Plots
High-quality plots summarizing structural and dynamic properties such as RMSD, RMSF, hydrogen bonds, PCA, cluster distributions, and more.
Binding Free Energy Report (if applicable)
If included in the project, you'll receive MM/PBSA or MM/GBSA energy decomposition reports with per-residue contributions.
Final Report (PDF)
A comprehensive summary detailing simulation setup, run parameters, analytical results, visual outputs, and key insights—with figures ready for publication or internal presentation.
| Use Case / Research Goal | Recommended Method | Why |
| Predict static binding pose between a ligand and protein | Molecular Docking | Fast and efficient for initial screening, but lacks time-dependent info |
| Validate docking pose, analyze binding stability over time | Molecular Dynamics (MD) | Captures induced fit, water mediation, and conformational adaptation |
| Analyze conformational changes or loop movement | MD Simulation or Normal Mode Analysis (NMA) | NMA gives general motion trends; MD provides atomic-level dynamics |
| Simulate very large systems (e.g. virus capsids, full membranes) | Coarse-Grained MD | Reduces atomic detail to improve simulation speed for large assemblies |
| Explore rare events (e.g. ligand unbinding, folding transitions) | Enhanced Sampling MD (e.g., aMD, metadynamics) | Accelerates slow transitions beyond classical MD reach |
| Calculate reaction mechanisms or covalent bond breaking/forming | QM/MM Hybrid Simulation | Required for electronic-level processes and metal center modeling |
| Quickly scan conformational flexibility of a small molecule or peptide | Monte Carlo (MC) Simulation | Efficient sampling of large conformational space with less computation |
| Assess residue flexibility or domain movement trends without full MD | Normal Mode Analysis (NMA) | Provides low-cost insight into flexible regions |
Can MD simulations help if I don't have any experimental structure?
Yes. We support model generation using AlphaFold2 or homology modeling. While simulations based on predicted structures may carry more uncertainty, they can still yield valuable insights—especially for comparative analysis or design screening.
What types of systems are difficult or not recommended for MD?
Highly disordered proteins, extremely large complexes (>1 million atoms), or systems involving covalent bond formation may not be ideal for classical MD. In such cases, coarse-grained modeling, enhanced sampling, or QM/MM approaches may be more appropriate.
Will I need to interpret the simulation results myself?
Not alone. Our team provides clear analytical outputs with visualizations and interpretation. If needed, we also offer consultation to help you extract key findings and integrate results into your research narrative.
How do you ensure the simulation is biologically relevant?
We configure every system based on known experimental conditions—such as pH, ion concentrations, and membrane composition—and apply validated force fields. If relevant, we can integrate cryo-EM maps, NMR restraints, or mutational data to enhance realism.
Can I run follow-up simulations later using the same system?
Yes. All simulation input files and configurations are provided, allowing you to run extensions or variants in-house or through us. Many clients start with a short run and later request extended trajectories or mutation variants.
Knowledge Center
Knowledge Center
Knowledge Center
Knowledge Center
Knowledge Center
Knowledge Center
Knowledge Center
Knowledge Center
Knowledge Center
Knowledge CenterOnline Inquiry