Scripts Reference

The following automation scripts are provided in the tutorial repository under tutorial/.

Pre-processing

pre-processing/1-amber-pre-run.sh

Runs the full classical and QM/MM minimisation/equilibration pipeline (Steps 1–5: MM minimisation, thermalisation, equilibration, SQM-MM and QM-MM energy minimisation).

pre-processing/2-amber-qm-vs-hirs-chrgs.sh

QM/MM MD runs using Gaussian as the external QM package; captures Hirshfeld CM5 charge log files at each step.

pre-processing/2-amber-qm-vs-vdd-chrgs.sh

QM/MM MD runs using TeraChem as the external QM package; captures VDD charge output files at each step.

Simulations

simulations/3-amber-tc-prod.sh

Runs three independent 5 ps QM/MM production simulations using TeraChem.

simulations/4-amber-tc-smd-hy-1.sh

Runs 95 independent QM/MM SMD simulations for the hydride-transfer CV, randomly selecting starting configurations.

simulations/nbo/5-amber-tc-nbo-smd-hy-1.sh

Runs 5 QM/MM SMD simulations (indices 96–100) coupled with NBO analysis; saves .47 NBO input files at each step.