Frequently Asked Questions
- On double-clicking on the Kisthelp java icon (kisthelpXXXX.jar), it causes the file to be opened in the archive manager instead of being executed: right-click the icon and select to open it with the JRE ("Java Runtime Environment")
- The program always freezes when I do TST calculations when reading frequencies values : The imaginary
frequency must be entered as "3000i" and not "-3000" in the .kinp input file. Whenever possible, the best is to let KiSThelP read
the quantum chemistry outputfile (Gaussian, NWCHEM, Gamess, ORCA, MOLPRO).
- I want to know if kisthelp do some rate calculation using gaussian outfile by CBS-QB3 method ? because cbs-qb3 method does not output frequency files separately. This kind of method (CBS) performs multi-job calculations. Such composite approach will combine the results of several calculations so that the KiSThelP parser cannot read the associated output file. However, in that case, you can manually build (see KiSThelP documentation) the KiSThelP input file (.kinp) so that
to select the appropriate potential energy, the appropriate vibrational frequencies ...
I have a question regarding the RRKM calculations for which I could not find the answer in your paper, https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.23470. For RRKM rate constant (Equation 21 in the paper), effective collision frequency (ω) is found through ω=βc ZLJ [M] in the program. Can you please let me know the expressions for the two terms, βc and ZLJ (collisional efficiency and Lennard–Jones collision frequency), as I could not find them in the paper.
βc corresponds to a numerical value representing the collisional efficiency. In our paper [E. Henon et al., Phys. Chem. Chem. Phys. 5 (2003) 5431] we decided to choose βc=0.2 for N2 and for the formaldehyde. For more details please refer to the paper by J. Troe J. Chem. Phys. 66, 4745 (1977). Z_LJ is defined in the paper by Troe and it is a function of the Lennard Jones diameters and potential wells, we used equations (3.1) and (3.3) of the Troe reference [J. Chem. Phys. 66, 4758 (1977)]. Some of these
parameters can be found in the KiSThelP menu Data/Lennard-Jones parameters for many species or analogues.
I just want to ask what Gaussian input should I use for the TS or IRC in KisTHelp? I tried the Opt + Freq QST and TS berny log files but its not working....
The TS (Transition State) requires a prior specific small Kisthelp treatment, and you are not allowed to supply a Gaussian .log (.out) for a TS during a rate constant calculation in Kisthelp
Actually, since Kisthelp also handles the Variational TST theory (VTST), the TS cannot longer be viewed as a stationary single point but rather as a reaction path: multiple points along the reaction path. From a practical point of view,
this concept of « reaction path » has been generalized in Kisthelp, even for the simple TST theory, which only requires a single point to describe
the TS. That is the reason one, prior to perform the TST or VTST calculation, or RRKM calculation, you need to build for the TS a specific single input file encapsulating the information for EVERY point along the reaction path (but not reacting nor product),
even though for the simple TS theory
this reaction path will reduce to a single point. For each point along the reaction path, this .kinp input file will, in addition to the other properties (vib. frequencies, mass, inertia moments, ...), contain the value of the intrinsic reaction coordinate for this point (needed for VTST treatment). Of course, for a single TS point, this input file reduces to one point and the IRC value to supply is 0.0.
To help you, Kisthelp provides the user with the « Data/Build Reaction path .kinp » tool. For simple TST calculations, you will have to enter « 1 » to the question « number of points to be read » and next supply the .log filename associated with your TS. Have a look at the video tutorial: http://kisthelp.univ-reims.fr/download/2tuto.mov
This should fix your problem.