jagarridotorres / rmsd_pp_ts

Locate TS based on RMSD-PP method

RMSD_PP_TS

Locate TS based on RMSD-PP method

Usage

To run a TS search

• Create dataframes and save them as .pkl to store the results of succesful runs (success.pkl) and failed runs (fail.pkl)
• Create folder to run the calculations (e.g. mkdir test_run)
• The following files should be present in the created folder
  • path.inp containing parameters defining the RMSD-PP run
  • reaction.xyz containing the geometry of the reactant
  • product.xyz containing the geometry of the product

The run can now be initiated from within the test_run folder by:

rmsd_pp_ts.py reactant.xyz product.xyz success.pkl fail.pkl

Depency on external programs

The procedure relies on external programs to do the quantum chemical calculations. In particular, there are calls to four different submit scripts (submitting xTB and Gaussian16 calculations) within rmsd_pp_ts.py:

xyz2mol

xyz2mol is used to calculate adjacancy matrices and SMILES from .xyz files

https://github.com/jensengroup/xyz2mol

submit_xtb_path:

Submits an RMSD-PP GFN2-xTB calculation for

• reactant structure: reactant.xyz
• product structure: product.xyz
• push value: k_push
• pull value: k_pull
• alpha value (width of Gaussian biasing potential): alp

The file path.inp must be present in the directory
When called separately, the usage is as follows:

submit_xtb_path reactant.xyz product.xyz k_push k_pull alp

submit_batches_xtb:

Submits all .xyz files in the current directory to single point energy calculations using the xTB program The jobs are submitted to slurm in batches
When called separately, the usage is as follows:
Go to the directory with the .xyz files to be submitted and call

submit_batches_xtb

submit_batches_gaussian:

Works as submit_batches_xtb except that the single point energy calculations are done using Gaussian 16, and instead of .xyz files it submits all gaussian input files (.com file) in the present directory.

submit_gaus16:

Submits a Gaussian16 calculation with the type of calculation, structure and method stated in the input .com file
When used separately, the usage is as follows:

submit_gaus16 input.com

The four submit scripts used can be found in submit_scripts