All-Atom & Coarse-Grained MD Simulation Service

Molecular Dynamics (MD) simulation serves as a cornerstone computational tool in scientific research, enabling researchers to observe and analyze the dynamic behavior of molecular systems at scales inaccessible to traditional experimental techniques. All-Atom (AA) and Coarse-Grained (CG) MD simulations represent the two primary approaches to this method, each tailored to address distinct research questions by balancing atomic resolution and computational efficiency. Both techniques rely on classical mechanics to solve Newton's equations of motion for molecular systems, but they differ fundamentally in the level of detail with which they model atomic interactions— a difference that dictates their applications, strengths, and limitations in scientific inquiry.

What is All-Atom MD Simulation?

All-Atom (AA) MD Simulation models every atom in a molecular system—including biomolecules (proteins, nucleic acids, lipids), solvents (water, organic solvents), and auxiliary molecules (ions, ligands)—as individual particles. It calculates interatomic forces (covalent bonds, electrostatic interactions, van der Waals forces, hydrogen bonds) using validated force fields (e.g., AMBER, CHARMM, GROMACS) parameterized to match experimental data, with femtosecond (10^-15 seconds) time steps to accurately capture rapid atomic vibrations. This detail enables observation of subtle phenomena like protein-ligand hydrogen bonds, enzyme active site flexibility, and mutation impacts. For example, AA simulations of amyloid-β (Aβ 42) using the AMBER ff19SB force field and OPC water model revealed how disulfide bonds alter its secondary structure and aggregation, aligning with experimental NMR chemical shift data.

What is Coarse-Grained MD Simulation?

Coarse-Grained (CG) MD Simulation simplifies systems by grouping atoms into functionally distinct "beads," reducing particles by 10x or more while retaining key physical/chemical properties (hydrophobicity, charge, shape). Beads may represent entire amino acids, lipid carbon groups, or water clusters, enabling larger time steps (picoseconds to nanoseconds) and larger systems (millions to billions of atoms) over longer time scales (milliseconds to seconds) than AA simulations. The Martini 3 force field, for instance, is widely used to study lipid bilayer and membrane protein dynamics—capturing large-scale interactions infeasible with AA methods. In nucleosome research, CG simulations using the SIRAH force field accurately replicate DNA structural parameters while enabling broader conformational sampling than AA simulations.

Our Services

Eata Simulation delivers comprehensive computational capabilities spanning the full spectrum of molecular dynamics methodologies. Our infrastructure supports investigations ranging from small molecule thermodynamics to massive biomolecular assemblies, with computational resources scaled to project requirements.

Standard Molecular Dynamics Simulations

Our fundamental service offerings include canonical ensemble (NVT) and isothermal-isobaric ensemble (NPT) simulations for both all-atom and coarse-grained systems. These services provide equilibrium sampling of molecular configurations, enabling calculation of thermodynamic averages, structural distributions, and dynamic correlation functions.

For all-atom systems, we support explicit solvent representations using established water models, with options for neutralizing ion addition and buffer salt concentrations matching experimental conditions. Simulation durations are tailored to convergence requirements for specific observables, with statistical uncertainty quantification.

Coarse-grained standard simulations access extended timescales for large systems, including membrane patches containing thousands of lipids, protein-membrane complexes, or polymeric materials. We advise on appropriate force field selections based on chemical composition and target properties.

Enhanced Sampling and Free Energy Calculation Services

We provide specialized capabilities for investigating rare events and quantifying free energy landscapes. Umbrella sampling services deliver potential of mean force calculations along specified reaction coordinates, with statistical error estimation and convergence verification.

Metadynamics implementations employ carefully selected collective variables to accelerate sampling of slow degrees of freedom. We offer well-tempered and bias exchange variants optimized for specific system characteristics.

Free energy perturbation (FEP) and thermodynamic integration (TI) services calculate relative binding affinities, solvation free energies, and conformational free energy differences with rigorous statistical mechanics foundations. These calculations require careful protocol design including appropriate lambda scheduling and overlap verification between adjacent states.

System-Specific Specialized Services

Membrane systems receive particular attention given their biological significance and simulation complexity. We provide services for building heterogeneous membrane models with specified lipid compositions, inserting membrane proteins with correct orientations, and simulating under appropriate surface tension or lateral pressure conditions.

Nucleic acid simulations require specialized force fields and careful treatment of electrostatics given the high charge density of phosphate backbones. We offer services for DNA and RNA systems including hybridization studies, quadruplex investigations, and nucleosome dynamics.

Protein-ligand interaction studies combine docking preparation, binding pose refinement through molecular dynamics, and binding free energy estimation. We support investigation of induced fit effects, allosteric modulation, and selectivity determinants across target families.

Materials science applications benefit from specialized treatments including amorphous cell construction for polymers, crystal surface preparation for mineral systems, and interfacial models for composite materials.

Optional Service Items

For all-atom investigations, we provide systematic simulation setup including system preparation, force field assignment, solvent addition and equilibration, production run execution, and trajectory analysis. Our protocols ensure proper treatment of protonation states, stereochemistry, and post-translational modifications. We implement appropriate boundary conditions, electrostatics treatments, and thermostat/barostat selections matched to specific ensemble requirements.

Coarse-grained services encompass model selection consultation, mapping scheme optimization, and parameter validation. We assist in determining appropriate resolution levels for specific research questions—whether atomistic detail is essential or whether coarse-grained representation suffices. Our workflows include systematic equilibration protocols and rigorous analysis of structural and dynamic properties.

If you are interested in our services and products, please contact us for more information.