MolAgent

Capabilities

MolAgent covers the main branches of molecular and materials simulation and works with the codes research groups already use. Procedures are added and validated together with early-access users, and a code you rely on can be added.

Branches and software

Typical studies in each branch, and the codes the agent prepares, runs and analyses. Commercial codes such as Gaussian, VASP or Q-Chem run under your own licence.

Quantum chemistry

Molecules and clusters with DFT and wavefunction methods.

  • Conformer search and geometry optimisation
  • Frequencies, thermochemistry and reaction energies
  • Transition states and reaction paths
  • Excited states and UV-vis spectra
  • IR, Raman and NMR spectra
  • Interaction energies, charges and electrostatic potentials
  • Gaussian
  • ORCA
  • Q-Chem
  • Psi4
  • PySCF
  • NWChem
  • TURBOMOLE
  • Molpro
  • xtb
  • CREST

Periodic DFT, solids and surfaces

Crystals, surfaces, interfaces and 2D materials with plane-wave and localised-basis DFT.

  • Lattice parameters, equations of state and elastic constants
  • Surface energies, adsorption and coverage
  • Band structures, densities of states and band alignment
  • Point defects, dopants and charge transition levels
  • Phonons and finite-temperature properties
  • Reaction barriers and ab initio molecular dynamics
  • VASP
  • Quantum ESPRESSO
  • CP2K
  • CASTEP
  • ABINIT
  • FHI-aims
  • GPAW
  • SIESTA
  • Phonopy

Molecular dynamics

All-atom simulations of liquids, solutions, polymers, interfaces and biomolecules.

  • System building, solvation and equilibration
  • Densities, heats of vaporisation and other bulk properties
  • Radial distribution functions, coordination and order parameters
  • Diffusion, viscosity and ionic conductivity
  • Interfaces, wetting and adsorption from solution
  • Polymer packing, crosslinking and glass transition
  • GROMACS
  • LAMMPS
  • OpenMM
  • AMBER
  • NAMD
  • DL_POLY

Free energies and enhanced sampling

Binding, solvation and phase behaviour, and events too rare for plain molecular dynamics.

  • Solvation and transfer free energies, partition coefficients
  • Absolute and relative binding free energies
  • Potentials of mean force by umbrella sampling
  • Metadynamics and related methods for rare events
  • Solubility and phase behaviour
  • PLUMED
  • GROMACS
  • OpenMM
  • AMBER
  • OpenFE
  • pymbar
  • alchemlyb

Coarse-grained and mesoscale models

Larger systems and longer times, with groups of atoms represented as single beads.

  • Martini 3 mapping and parameterisation
  • Bottom-up models from atomistic simulations: iterative Boltzmann inversion, force matching
  • Self-assembly of surfactants, lipids and block copolymers
  • Polymer melts and blends
  • Dissipative particle dynamics for mesoscale fluids and soft matter
  • Back-mapping to atomistic resolution
  • GROMACS
  • LAMMPS
  • HOOMD-blue
  • ESPResSo
  • VOTCA

Machine-learned interatomic potentials

Near-DFT accuracy within their training domain, at a small fraction of the cost, for screening and long simulations.

  • Pre-screening of structures and adsorption sites with universal potentials
  • Fine-tuning on DFT data for a given chemistry
  • Training with active learning and uncertainty estimates
  • Validation against DFT: energies, forces, phonons, diffusion
  • Large-scale molecular dynamics with the fitted potential
  • MACE
  • CHGNet
  • SevenNet
  • MatterSim
  • UMA
  • Orb
  • DeePMD-kit
  • NequIP
  • Allegro

Force fields and parameterisation

Parameters for new molecules and materials, checked against reference data.

  • Assignment from GAFF2, OPLS-AA, CHARMM CGenFF and OpenFF
  • Partial charges: RESP, AM1-BCC, CM5
  • Torsion fitting to quantum-chemical scans
  • Validation against experimental densities, enthalpies and structures
  • Parameters for ions, metals and inorganic surfaces
  • AmberTools
  • OpenFF Toolkit
  • LigParGen
  • CGenFF
  • ForceBalance

Building, screening and analysis

The work around the calculations: structures in, numbers and figures out.

  • Molecules from SMILES, conformers and libraries
  • Crystals, slabs, supercells and interfaces
  • Polymer chains, amorphous cells and solvated boxes
  • High-throughput screening with job arrays and result databases
  • Trajectory analysis, statistics and figures
  • RDKit
  • Open Babel
  • ASE
  • pymatgen
  • Packmol
  • MDAnalysis
  • MDTraj
  • OVITO

Application areas

Five of these areas have an example study, with an interactive structure, on the Examples page.

Batteries and electrolytes

Solvation structure, transport and stability of electrolytes; electrode surfaces and interphases.

LiPF6 in EC:DMC

Catalysis and surfaces

Adsorption, reaction mechanisms and activity trends on metals, oxides and single-atom catalysts.

CO2 reduction on Cu(111)

Semiconductors and 2D materials

Defects, dopants, band alignment and interfaces in semiconductors and layered materials.

Sulfur vacancy in MoS2

Pharmaceuticals and formulation

Binding, solubility, permeation and excipient interactions of drug molecules.

Ibuprofen in β-cyclodextrin

Polymers, resins and composites

Curing, glass transition, mechanical response and interfaces in polymer materials.

DGEBA cured with DETA

Soft matter and interfaces

Surfactants, membranes, emulsions and self-assembly, from all-atom to coarse-grained models.

Checks at each step

Before it reports a result, the agent makes the checks an experienced practitioner would make.

Inputs

Charge, multiplicity and stoichiometry; overlapping atoms; box size against interaction cut-offs; units.

Quantum chemistry

SCF and geometry convergence; imaginary frequencies; spin contamination; sensitivity to the functional and basis set.

Periodic DFT

Cut-off and k-point convergence; slab thickness and vacuum; dipole corrections; magnetic states.

Molecular dynamics

Equilibration of energy, density and box; energy drift; sampling length, block-averaged uncertainties and finite-size effects.

Free energies

Overlap between neighbouring states; agreement between forward and reverse estimates; convergence with simulation time.

Failed jobs

Walltime, memory and convergence failures are diagnosed, and the job restarts from the last good point with adjusted settings.

Computing environments

MolAgent runs on the machines and software stack you already have.

  • Schedulers: SLURM, PBS Pro and OpenPBS, LSF, or none on a workstation.
  • Software: environment modules, Apptainer and Singularity containers, conda, Spack, or explicit paths.
  • Machines: cluster login nodes, workstations, servers and cloud virtual machines, on Linux or macOS.
  • Models: any supported provider account, or an open-weight model on your own server.

Early access

MolAgent is in alpha. We are installing it with a small number of research groups now; a private beta opens in 2027. Write to us with the systems you study, the codes you use and the machines you compute on.

Or write to contact@molagent.ai.