Starting with two molecular structure (reactant and product), ProfileRXN will first optimize them and interpolate a trajectory between the optimized geometries. NEB calculation will then be used to guide the trajectory towards the minimum energy pathway. Finally, a guessed transition state structure from the NEB calculation will be optimized and energies of reactant, product, and transition state will be written as a json file.
Author: Heejune Park
Contact Email: [email protected]
Commands below will create a conda environment and install ProfileRXN.
git clone [email protected]:hjnpark/ProfileRXN
cd ProfileRXN
conda update conda
conda env create -f ProfileRXN_env.yaml
conda activate ProfileRXN
pip install -e .Setting up the environment might take some time.
Install next branch of QCFractal:
https://github.com/MolSSI/QCFractal/tree/next
Following commands will install the QCFractal's next branch.
git clone -b next [email protected]:MolSSI/QCFractal.git
cd QCFractal
pip install -e qcportal/ -e qcfractalcompute/ -e qcfractal/Install neb branch of geomeTRIC:
https://github.com/hjnpark/geomeTRIC/tree/neb
git clone -b neb [email protected]:hjnpark/geomeTRIC.git
cd geomeTRIC
pip install -e .Done!
profile-rxn -h will show all the available arguments. Input xyz file should have two geometries. If it has more than two, the first and last frame will be used.
exmaples/bash.sh shows an example command.
- Perform vibrational frequency analysis and calculate Gibbs free energies.
- IRC step needs to be added.