QRC: Quick Reaction Coordinate

Documentation

Transition states must be identified and frequency calculations completed. The Java code here will automatically recognise Jaguar and GAMESS output.

FreqQRC
This program generates structures distorted by the specified frequency:

FreqQRC FILENAME [scale] [-f#]

FreqQRC requires a FILENAME corresponding to the output of a frequency calculation. Optionally, it may be given a scale a floating point number to scale the distortions introduced in the new structures (default 1.0). By default the first frequency is used but the -f flag, immediately followed by an integer (-f2, -f3), will use a higher frequency. Only the first few frequencies are available.

FreqQRC produces a new file FILENAME.fdt

FindQRC
This program takes the output from a minimisation of the structures generated by FreqQRC.

FindQRC FILENAME.out [FILENAME.fdt] [-u]

This creates a new file flatfreq_add.qrc. The first column is the energy of each structure, and the next columns are different ways of measuring the distance between adjacent structures. The second column is mass-weighted rms distance from the starting structure, and we have found this to be the most effective. The third column gives the sum of the distances between adjacent structures, and is similar but slightly larger. The fourth and fifth columns are non-mass-weighted versions of the second and third.

The .fdt file can be omitted, and the calculation reports distances from the first distorted structure instead of the undistorted structure held in this file.

By default, FindQRC omits points for which the energy goes up as the minimisation progresses. Occasionally it can be useful to visualise these points too, and this can be done using the -u flag:

Cyclohexane example