examples

Examples

This directory contains six examples to use factorpol package.

Notebooks

1. 00-generate-qm-reference.ipynb

   This example is used to generate QM reference data for trainingset. The QM reference data is used to calculate the difference between QM and MM energies. The difference is used to optimize polarizability parameters.

2. 01-derive-polarizability.ipynb

   This example is used to optimize polarizability parameters for a trainingset using "Nelder-Mead" optimizer.

3. 02-RESP-dPol.ipynb

   This notebook provides an example to generate RESP-dPol partial charges.

4. 03-AM1-BCC-dPol.ipynb

   This notebook provides an example to generate AM1-BCC-dPol partial charges.

5. 04-parameterize-for-simulation.ipynb

   This example is used to generate force field file for OpenMM and MPID plugin

6. 05-optimize-pols-vdiff.ipynb

   This example is used to optimize polarizability parameters for a trainingset without using "Nelder-Mead" optimizer.

Relevant data

Polarizability: ret_alphas.csv

Bond charge correction with polarizability: ret_bccs.csv

Force field .xml for OpenMM and MPID plugin: forcefield.xml