Force-field optimization

• This project is part of an integrated scheme for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumeration.

• The main steps of the scheme, referred to as CombiFF, are:

  1. definition of a molecule family;
  2. combinatorial enumeration of all isomers;
  3. query for experimental data;
  4. automatic construction of the molecular topologies by fragment assembly;
  5. iterative refinement of the force-field parameters considering the entire family.

J. Chem. Theory Comput., 16, 7525-​7555 (2020).

• This project is only concerned about topic (iv).

• There are two key aspects in this scheme:

  1. The force-field design relies on an electronegativity-equalization scheme for the atomic partial charges (J. Chem. Phys. 131, 044127 (2009)).
  2. The optimization procedure uses statistical-mechanical expressions.

Files Description

The script files are found in the scr/ directory.

Required directories:

• bin/: Directory with SAMOS executable.

• scr/: Directory with source code.

• wrkDir/: working directory at the same level of the scr/ directory. Run the pipeline from this directory.

• wrkDir/00_inp/: Directory of input files.

  • mol.dat: File with list of molecules.
  • Conf.dat: Configuration file.
  • listAtom.dat: File with list of atoms for each molecule.
  • listAng.dat: File with list of angles for each molecule.
  • listBond.dat: File with list of bonds for each molecule.
  • matrix.dat: File that specifies usage of C12(II) Lennard-Jones parameters.
  • model.sam: Template of SAMOS input file.
  • prm_0.dat: File with initial guess of parameters.
  • symmetry_sig.dat: File that specifies which parameters are optimized simultaneously in terms of sigma.
  • symmetry_eps.dat: File that specifies which parameters are optimized simultaneously in terms of epsilon.

• wrkDir/cfg/: Directory with configurations.

  • 00_{molecule_cod}_liq_ini.cfg: Default configuration in the liquid phase.
  • 00_{molecule_cod}_gas_ini.cfg: Default configuration in the gas phase.

• wrkDir/top/: Directory with topologies.

• wrkDir/trc/: Directory with trajectories.

• wrkDir/prm/: Directory with default IFP file:

  • FILE.ifp: Default interaction parameter file (IFP).

Installation

This pipeline uses Python 3.7 and default packages for data visualization and statistical analysis.

Additional packages:

• scipy

Usage

These are the options:

• GEN: generate param.mod files to run simulations.
• ANA: perform analysis of the simulation results.
• OPT: optimize force-field parameters.
• SUB: submit jobs to run on euler.
• PLOT: plot main simulation results.

Execute the pipeline with the following command:

python $PATH/run.py $OPTION $IT

where PATH = path to source code OPTION = (GEN, ANA, OPT, SUB, PLOT) and IT is the iteration number.