Software

Many of the group’s developments are implemented and available in CHARMM (CHemistry at HARvard Molecular Mechanics), including

  • MS-ARMD (reactive molecular dynamics simulations)
  • MMPT (molecular mechanics with proton transfer)
  • MS-MMPT (proton transfer in bulk)
  • MTP (multipolar force fields)
  • DCM (discrete charge model for multipolar simulations)
  • RKHS+F (reproducing kernel with forces for accurate bonded interactions)
  • PINS (partial infinite swapping)
  • XTBD (extended bond – replace harmonic terms with more sophisticated stretch potentials, such as “Morse”, or “reproducing kernel”)

Git Repository

Various software projects completed by the group are made available via the group’s Git repository:

https://github.com/MMunibas

A complete list of software is available there, projects include:

  • FittingWizardWeb1: A Java-based WebApp that assists the user in fitting force field parameters to Quantum Chemistry and Molecular Dynamics reference data
  • Physnet2: Code for training PhysNet models for neural-network-based molecular dynamics simulations
  • Briz3: A collection of Python utilities to assist with fitting multipolar charge models for use with CHARMM’s MTPL module
  • MDCM4: Differential-Evolution-based fitting code to create minimal distributed charge models for use with CHARMM’s DCM module
  • RKHS5: Fortran90 implementation of the reproducing kernel Hilbert space (RKHS) method

References

  1. F. Hédin, K. El Hage and M. Meuwly
    A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations
    J. Chem. Inf. Model. (2016) 56, 1479
  2. O. Unke and M. Meuwly
    PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges
    J. Chem. Theory Comput. (2019) 15, 3678
  3. T. Bereau, C. Kramer and M. Meuwly
    Leveraging Symmetries of Static Atomic Multipole Electrostatics in Molecular Dynamics Simulations
    J. Chem. Theory Comput. (2013) 9, 5450
  4. O. Unke, M. Devereux and M. Meuwly
    Minimal distributed charges: Multipolar quality at the cost of point charge electrostatics
    J. Chem. Phys. (2017) 147, 161712
  5. O. Unke and M. Meuwly
    Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces
    J. Chem. Inf. Model. (2017) 57, 1923