Simulation basename:
The Gaussian input file will be called $basename.com,
the checkpoint file $basename.chk.
Checkpoint file based on:
- If you want to use info like coordinates or the initial guess for
the wave function from a previous checkpoint file you can specify the
filename here. The file will be copied to $basename.chk and the latter
is used for the simulation. (The reason for copying is that checkpoint
files are overwritten in subsequent simulations and you might want to
keep the previous file)
Number of processors:
Number of CPUs requeste for the simulation (%nproc entry in Gaussian).
Memory:
Total memory requested for the simulation (%mem entry in Gaussian).
Simulation type:
Choose among Single point calculations, geometry optimizations and
frequency calculations. For force constants 'Frequency' must be
chosen.
Method:
Choose amongst a number of simulation methods like HF, UHF or
B3LYP from a list. If your desired method is not included you can
specify it in the 'other keywords field. For metal containinig systems
you should use a DFT method (e.g. B3LYP) while for organic
molecules Hartree-Fock (RHF) is fine. For open-shell systems you must
use unrestricted methods (UHF, UB3LYP,...).
Wavefunction:
Choose a set of wavefunctions from the list. If the desired one is not
included, you can specify it in the other keywords field. For most
force field applications 6-31G* is fine. Note that method and wave
function for single point runs and geometry optimization must be
identical otherwise your force constants will most likely be rubbish
because you are taking the Hessian not at the minimum of the energy function.
Geometry taken from:
The initial geometry can be taken either from the checkpoint file or
specified explicitely as Z-matrix (in the form of cartesian
coordinates). It is recommended to choose the latter because when the
cartesian coordinates are included in the setup file you can
reload the file later without previously loading a molecule in VMD.
Initial wavefunction:
The initial guess of the wavefunction can be computed from scratch using
the Harris method (this is Gaussians default) or read from the
checkpoint file. If both geometry and initial guess are taken from
checkpoint file (Gaussian keyword Geom=AllCheck), then no total charge
and multiplicity can be defined and the respective fields are
inactivated.
Coordinates for Opt/Freq:
Choose between the redundant internal coordinates autogenerated by
Gaussian, the explicitely defined internal coordinates from Paratools
list or modified autogenerated redundant internal coordinates.
For optimizations 'internal (auto)' is recommended and for force
constant determination usually 'internal (explicit)' is chosen.
Solvent:
You can specify a solvent (i.e. a dielectric constant) in case you are
using the polarizable continuum (PCM) solvent model. (Not useful for
PARATOOL, don't choose anything)
PCM method:
Choose the method used for the polarizable continuum model.
(Not useful for PARATOOL, don't choose anything)
Charges:
Use the checkbuttons to specify if you want to compute ESP charges of
NBO charges additionally to the Mulliken populatin analysis.
Other keywords:
Add any Gaussian keywords to the setup file.
Total charge:
The charge of your entire system. Check this value Paratool's guess
depends on many factors and my be wrong.
Multiplicity:
The mulitplicity of your system. You must specify this manually
Paratool can guess it by n means.