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Forcefield parameterization plans

Michael Shirts edited this page Jul 17, 2014 · 7 revisions

Christopher: How would work be distributed? Need to be very focused about time put into it

Methodology improvements to ForceBalance:

  • more efficient: reweighting; can we speed up from 6 weeks on 200 GPUs to 6 hours?
  • Bayesian sampling

Questions to address:

  • for traditional functional forms, what can we do to improve parameters?
  • What kinds of datasets do we need?
  • Can we explore new functional forms?
  • How do we handle atom types?

Desiderata:

  • Want a consistent set of nonbonded parameters, not special parameters for solvents.

Useful data:

Christopher is interested in small molecule forcefield with the following properties:

  • start with neat and mixed solvents
  • simultaneous fitting of all solvents
  • bond charge increment model for fast corrected semiempirical-derived charges
  • sigma hole on C-Cl / bond-centered charges in general, but judiciously chosen (MRS has reweighting scheme for bond length changes that may prove useful)
  • scaling factors for 1,4 torsions would be an adjustable parameter
  • bond lengths and valence angles aren't going to make a huge difference, but we may want to choose them to be close to some QM reference to allow for good QM/MM overlap
  • would like to allow decoupling of parameter types for nonbonded, bonds, angles, torsions (VSP: could be implemented in traditional codes with combinatorial atom types)

Data to fit:

  • QM calculations: torsion drives
  • excess densities as a function of mole fraction and temperature (to be collected by JDC)
  • radial distribution functions from scattering experiments (or scattering data directly); how do we measure these?
  • excess molar enthalpies: calorimetry can do this; heats and heat capacities of mixtures of liquids (see work by Paul Smith, Kansas state)
  • need database of simple compounds, but compounds we need in database will change with atom types
  • NMR for torsions? (KAB working on this)
  • organic crystals from CCDC?

Atom typing:

  • inspired by Alan Mark using error as a function of (sigma, epsilon)
  • Christopher has SMARTS-based atom typing scheme for parm@frosst (LPW has this)
  • atom typing has to take into account bond order
  • create/destroy bond types?

Comparisons:

Identify what data we need to improve forcefield

JDC will work with Christopher Bayly to get atom type sampling running

Starting set of molecules?

  • DrugBank?
  • all possible molecules up to N atoms?
  • simple liquids we can buy? nontoxic if possible Curate with Christopher Bayly

The path forward:

  • Christopher Bayly will come up with a few hundred molecules as SMILES strings for some initial QM calculations
  • Christopher will come up with base types and decorators, send along parm@frosst examples
  • We will work with Lee-Ping Wang to do some QM calculations; lots of torsion drives
    • QM model for torsion scans must be doable by other people: DFT/6-311+G(d,p) (dispersion-corrected)
    • GAMESS would be nice (or Qchem, or quantum espresso, etc.)
    • do different quantum packages come up with same potential?
    • 30-degree increments is good, but have to get to all minima
    • go around one way and then reverse to avoid hysteresis
    • barrier heights don't have to be that detailed, but have to get all minima
  • John Chodera will send Christopher a list of simple liquids we can buy to select optimal subset

Look into:

  • what QM package can we put on FAH?