All-Atom Molecular Dynamics & Atomistic Biophysics
Capture conformational transitions, characterize cryptic binding pockets, and calculate binding free energy landscapes. GPU-accelerated molecular dynamics simulations engineered in GROMACS and AMBER.
Computational Simulation Capabilities
Our biophysicists model complex biomolecular architectures across solvated microenvironments:
Simulation Architectures
- All-atom explicit solvent simulations (TIP3P, OPC water models)
- Lipid bilayer embedded systems (POPC, POPE, cholesterol mixtures)
- Macromolecular complexes: Protein-Protein, Protein-RNA, Protein-Small Molecule
Force Fields & Engines
- CHARMM36m and AMBER ff19SB parameterizations
- General AMBER Force Field (GAFF2) and CGenFF for novel chemical ligands
- NVIDIA A100/H100 accelerated GROMACS 2024 production runs
Analytical Post-Processing & Trajectory Metrics
We extract biophysical insights from raw trajectory gigabytes using rigorous statistical mechanics:
- Structural Convergence & Plasticity: Time-dependent Root-Mean-Square Deviation (RMSD), per-residue Root-Mean-Square Fluctuation (RMSF), and Radius of Gyration (Rg) to verify structural equilibration.
- Essential Dynamics & PCA: Covariance matrix diagonalization and Principal Component Analysis to identify dominant slow-frequency conformational motions.
- Temperature-Targeted MD (TTMD): Controlled thermal unfolding simulations to expose instability hotspots and engineer stabilizing mutations for industrial enzymes and therapeutic antibodies.
- Binding Free Energy Decomposition (MM-PBSA / MM-GBSA): Residue-level energy decomposition to determine which amino acid side chains contribute most to binding affinity or resistance.
Turnaround & Deliverables Package
Within 3 to 5 weeks depending on simulation duration (100ns to 1μs), clients receive:
- Full trajectory coordinate archives (`.xtc`, `.dcd`) alongside cleaned starting topologies (`.gro`, `.top`, `.prmtop`).
- High-definition 4K rendering videos of ligand dissociation, binding pocket breathing, or domain transitions.
- Comprehensive thermodynamic reports with free energy convergence plots and standard error estimations.
- Jupyter notebooks containing the reproducible Python analysis scripts (MDTraj, MDAnalysis, ProDy).
Scope Your Molecular Dynamics Study
Discuss your protein structure, ligand parameters, and simulation nanosecond requirements with our computational biophysicists.
Submit Technical Scoping Inquiry →