Molecular dynamics
All-atom molecular dynamics
Run atomistic protein simulations with explicit force-field, solvent, ensemble, and trajectory settings.
What is all-atom molecular dynamics?
All-atom molecular dynamics is a simulation method that represents every modeled atom explicitly and calculates its motion under an atomistic force field. Hydrogen atoms may be explicit even when constrained bonds permit a larger timestep. Atomistic resolution supports detailed interaction analysis, but it increases system size and does not eliminate limitations in parameterization or conformational sampling.
Choose all-atom MD when local interactions, hydration, side-chain rearrangements, salt bridges, or ligand contacts matter. Confirm that every residue, cofactor, ion, ligand, terminus, and modification has compatible parameters; an apparently complete coordinate file is not necessarily a complete topology.
ProteinIQ can run GPU-accelerated OpenMM simulations for proteins and optionally protein–ligand systems with AMBER or CHARMM protein force fields and explicit or implicit solvent. The focused template prepares a protein and configures an all-atom AMBER simulation; specialized components still require validated parameter files.
When to use all-atom molecular dynamics
- Best fit. Detailed protein and protein–ligand conformational analysis
- Required evidence. Complete atomistic coordinates, compatible parameters, solvent model, ions, ensemble, and duration
All-atom molecular dynamics methods
Atomistic force fields assign bonded terms, partial charges, and van der Waals parameters to defined atom types. Long-range electrostatics, nonbonded cutoffs, water model, constraints, and integration timestep form part of the scientific method.
OpenMM accelerates the same physical model on GPUs but does not make every setup equivalent. Compare only simulations with compatible Hamiltonians and clearly document any ligand parameterization or custom force terms.
All-atom molecular dynamics applications
All-atom molecular dynamics is best suited to detailed protein and protein–ligand conformational analysis. Match the modeled system, timescale, resolution, and ensemble to the observable rather than choosing a protocol because it produces a longer trajectory or more elaborate figure.
Use simulation as model-based evidence. Connect trajectory observations to experimental data, alternative parameterizations, independent starts, and uncertainty whenever the downstream claim concerns mechanism, affinity, kinetics, stability, or population.
How to run all-atom molecular dynamics online
The connected workflow prepares the structure and runs the configured conventional simulation. Review every system and ensemble setting before submission.
- Audit atoms. Audit missing atoms, alternate locations, termini, modifications, ligands, cofactors, and protonation.
- Prepare topology. Choose mutually compatible protein, ligand, water, and ion parameters and preserve versions.
- Set ensemble. Set solvent, box, electrostatics, constraints, timestep, temperature, pressure, duration, and reporting.
- Run OpenMM. Run minimization, equilibration, and production with OpenMM and retain checkpoints and logs.
- Inspect details. Inspect stability, contacts, hydration, secondary structure, compactness, and replicate agreement.
How to interpret all-atom molecular dynamics results
Use atom-level detail selectively. Persistent hydrogen bonds and salt bridges should be reported with geometric definitions and occupancy; transient contacts need temporal context and uncertainty across replicas.
Representative snapshots are illustrations, not population estimates. Cluster or state populations require adequate sampling, a declared feature space, and sensitivity checks for alignment and cutoff choices.
Benefits of all-atom molecular dynamics
- Preserves atom-level interactions. Preserves atom-level interactions for projects focused on detailed protein and protein–ligand conformational analysis.
- Supports explicit hydration. Supports explicit hydration for projects focused on detailed protein and protein–ligand conformational analysis.
- Works with established force fields. Works with established force fields for projects focused on detailed protein and protein–ligand conformational analysis.
Limitations of all-atom molecular dynamics
- Computationally demanding. Computationally demanding. Address this with complete atomistic coordinates, compatible parameters, solvent model, ions, ensemble, and duration.
- Parameter coverage can fail. Parameter coverage can fail. Address this with complete atomistic coordinates, compatible parameters, solvent model, ions, ensemble, and duration.
- Timescale limits remain. Timescale limits remain. Address this with complete atomistic coordinates, compatible parameters, solvent model, ions, ensemble, and duration.
How all-atom molecular dynamics works
Prepare a protein with PDB Fixer and run OpenMM using an all-atom AMBER force field and explicit-solvent NPT settings.
- Audit atoms. Audit missing atoms, alternate locations, termini, modifications, ligands, cofactors, and protonation.
- Prepare topology. Choose mutually compatible protein, ligand, water, and ion parameters and preserve versions.
- Set ensemble. Set solvent, box, electrostatics, constraints, timestep, temperature, pressure, duration, and reporting.
- Run OpenMM. Run minimization, equilibration, and production with OpenMM and retain checkpoints and logs.
- Inspect details. Inspect stability, contacts, hydration, secondary structure, compactness, and replicate agreement.
Inputs and outputs
Check formats before running, then inspect and download the result from every workflow step.
Inputs
Simulation evidence
PDBmmCIFTPRGROXTCA protein PDB, ENT, or mmCIF file and, optionally, a compatible ligand parameter file.
Outputs
Simulation outputs
XTCPDBCSVJSONZIPOpenMM trajectory, final coordinates, logs, checkpoints, energies, and analysis-ready files.
Tools for all-atom molecular dynamics
Use these methods to prepare inputs, run the core analysis, inspect outputs, and validate the evidence described in this workflow.
OpenMM
Run GPU-accelerated all-atom protein or protein–ligand simulations
GROMACS
Run conventional protein molecular dynamics with classical force fields
MD Trajectory Analysis
Analyze compatible trajectories with structural and dynamical metrics
PDBFixer
Repair missing atoms and standardize structures before simulation
PDB2PQR
Prepare protonation, charges, and radii for structural review
PROPKA 3
Estimate pKa values and inspect protonation-sensitive sites
RMSD calculator
Compare representative structures with RMSD
Radius of gyration
Measure compactness for representative structures
DSSP
Assign secondary structure to representative protein conformations
SASA calculator
Calculate solvent-accessible surface area for exported structures
MolProbity
Validate representative protein conformations
gmx_MMPBSA
Estimate endpoint binding energies from compatible GROMACS trajectories
Other molecular dynamics workflows
Compare related approaches based on the molecular system, available evidence, required inputs, and decision you need to support.
Frequently asked questions
A protein PDB, ENT, or mmCIF file and, optionally, a compatible ligand parameter file.
OpenMM trajectory, final coordinates, logs, checkpoints, energies, and analysis-ready files.
Yes, for the conventional configuration described on this page. ProteinIQ runs the connected GROMACS or OpenMM workflow and returns the engine-native trajectory and result files. Advanced protocols still require separate method support.
There is no universal number. Use independent starts and enough sampling to evaluate the slow observables behind the claim. Report replicate-level results, blockwise stability, and uncertainty rather than pooling trajectories without checking agreement.
Retain coordinates, complete topology and parameters, force-field versions, solvent and ion models, ensemble controls, constraints, timestep, seeds, checkpoints, logs, and trajectory.
A complete all-atom molecular dynamics project is commonly quote-based because system preparation, parameterization, sampling length, replica count, analysis, and interpretation vary substantially. Current published examples span from $50 for a bounded 100 ns GROMACS simulation to a $5,000 minimum for a dedicated commercial molecular-dynamics engagement.
Those prices describe materially different deliverables, so compare the included preparation, validation, replicates, analysis, raw files, interpretation, and support—not only trajectory length. Membrane building, unusual residues or ligands, advanced sampling, and convergence assessment can dominate the real scope.
ProteinIQ self-service starts at $29 per month for academic Plus and $99 per month for commercial Pro, with the configured run estimated in credits before submission. Done-for-you molecular dynamics work is scoped separately when preparation, method design, external advanced sampling, or interpretation is required.
Start with a workflow you can inspect and edit
Add your inputs, review the settings, and keep every structure, score, table, and file connected to the step that produced it.