Quickstart: mlmm tsopt

Goal

Optimize a TS candidate and verify that it is a first-order saddle point.

Prerequisites

  • TS candidate geometry: ts_guess.pdb

  • MM topology: real.parm7

  • ML region definition: ml_region.pdb

1. TS optimization

mlmm tsopt -i ts_guess.pdb --parm real.parm7 --model-pdb ml_region.pdb \
 -q 0 -m 1 --out-dir ./result_tsopt

tsopt performs a final Hessian evaluation and imaginary-frequency check automatically at the end of optimization. Check the terminal output for lines like:

[Imaginary modes] n=1 ([-593.1])

Output validation

  • result_tsopt/final_geometry.pdb — optimized TS structure

  • result_tsopt/vib/ — trajectories for the imaginary-frequency normal mode (imag_*_trj.xyz, .pdb)

  • Terminal output: n=1 is required for first-order-saddle certification; inspect the mode displacement and IRC connectivity

2. (Optional) Separate frequency analysis

Run a standalone freq job when you need full vibrational frequency output or thermochemistry corrections (--thermo in the all command). If you only need the imaginary-frequency check, the tsopt output above is sufficient.

mlmm freq -i ./result_tsopt/final_geometry.pdb --parm real.parm7 --model-pdb ml_region.pdb \
 -q 0 -m 1 --out-dir ./result_freq

Tips

  • Compare Analytical and FiniteDifference runtime and memory on a representative target-system pilot.

  • To use a different MLIP backend, add -b orb (or mace, aimnet2). Default is uma.

  • Check full options with mlmm tsopt --help-advanced and mlmm freq --help-advanced.

Next step

  • Trace the path with irc, or run the end-to-end route with all.