Restarting KinBot or pes

Restarting KinBot or pes

Both with KinBot and through the pes script, it is possible to restart a calculation where it left off after a previous run. It is, however, important to keep certain parameters unchanged during restart, else there is no guarantee the code will run cleanly. A few things to keep in mind:

1. The numbering of atoms is key when running kinbot or pes. If pes is restarted from a well different from the initial one, the xyz structure should be used to define it. The SMILES do not preserve the atom order.
2. Parameters that can be changed upon restart:

• homolytic_scissions
• barrier_threshold
• simultaneous_kinbot
• high_level (note that when using pes, the basis for the barrier_threshold is the high-level (L2) calculation, unless it was not requested)
• conformer_search (only switch this on if no high-level calculations are done yet, because otherwise the lowest energy structures are not propagated further in the calculations to L2 and L3)
• rotor_scan

A typical scenario is that pes is started without the high-level (L2) calculation, the conformer search and the rotor scans, to determine the general features and the complexity of the PES in a relatvely short amount of time. Once the key features and a good value for the barrier threshold are established, pes can be restarted with L2 and conformational search included.