Settings for QCxMS2

Settings of a QCxMS2 run can be changed via the following command line options:

qcxms2 [INPUT] [OPTIONS]

General Settings
Command	Description
`-h, --help`	Print an overview of most available options (i.e., more or less this site completely).
Runtype Options:
`-ei`	Compute an electron impact (EI) spectrum (default).
`-cid`	Compute a collission-induced dissociation (CID) spectrum.
`-esim`	Simulate only different IEE distributions for a given reaction network from a previous calculation.
`-oplot`	Plot only peaks from the previous QCxMS2 calculation.
General and Technical Options:
`-chrg [int]`	Give charge of the input molecule.
`-edist`	Choose distribution for IEE (“poisson” (default) or “gaussian”).
`-eimp0 [real]`	Specify impact energy of electrons in eV (default: 70).
`-eimpw [real]`	Specify width of energy distribution (default: 0.1).
`-ieeatm [real]`	Specify energy per atom in eV (default: 0.8), works only for EI mode.
`-esiatom [real]`	Specify energy per atom in eV, works only for CID mode.
`-esi [real]`	increase average internal energy in eV for CID mode (default 0.0)
`-esiw [real]`	Specify width of ionization energy distribution in eV, works only for CID mode.
`-nots`	Take reaction energy instead of barrier → no path search (quick mode for fragments).
`-T [integer]`	Select the number of overall cores (default: 4).
`-nfrag [integer]`	Select the number of subsequent fragmentations you want to simulate (default: 6).
`-pthr [real]`	Specify the intensity at which a fragment is further fragmented in % (default: 1%).

Quantum Chemical calculation settings
Options for QC Calculations:
`-nebnormal`	Use normal settings instead of loose settings for NEB search.
`-notsgeo`	Do not use geodesic interpolation as a guess for restarting non-converged NEB runs.
`-tsnodes [integer]`	Select the number of nodes for the path (default: 9).
`-geolevel [method]`	Method for geometry optimization and path search.
`-tslevel [method]`	Select level for computing reaction barriers.
`-iplevel [method]`	Select level for computing IPs for charge assignment.
`-ip2level [method]`	Select level for computing IPs for charge assignment of critical cases with close IPs (difference below 2 eV).

The default for all levels is GFN2-xTB. The following methods are available for all four different levels:

Keyword	QM Method	Program
gfn2	GFN2-xTB	xtb
gfn1	GFN1-xTB	xtb
r2scan3c	r2SCAN-3c	ORCA
pbeh3c	PBEh-3c	ORCA
wb97x3c	wB97X-3c	ORCA
pbe0	PBE0-D4/def2-TZVP	ORCA
pbe0matzvp	PBE0-D4/ma-def2-TZVP	ORCA

Note

The recommended settings are GFN2-xTB for geometry optimizations (-geolevel) and IP prescreening (-iplevel) and the efficient range-seperated hybrid wB97X-3c for barrier and energy calculations and refinement of close IPs (-tslevel and -ip2level). Using DFT for the geometry optimization is very expensive and only recommend for very small systems. For the prescreening of IPs, GFN2-xTB is more moste cases sufficient. However, for difficult systems, e.g., negative ions, DFT should be used. The hybrid functional PBE0-D4 with mininimal augmented basis set (pbe0matzvp) is recommended here both for -iplevel and -ip2level.

Further Settings
Options for Fragment Generation with CREST msreact:
`-msnoiso`	Sort out non-dissociated fragments in CREST msreact (i.e., rearranged structures).
`-msiso`	Sort out dissociated fragments in CREST msreact (i.e., rearranged structures).
`-msfulliso`	Allow rearrangements for subsequent fragmentations in CREST msreact (activated by default).
`-msnoattrh`	Deactivate the attractive potential between hydrogen and LMO centers.
`-msnshifts [int]`	Perform n optimizations with randomly shifted atom positions (default: 0).
`-msnshifts2 [int]`	Perform n optimizations with randomly shifted atom positions and a repulsive potential applied to bonds (default: 0).
`-msnbonds [int]`	Maximum number of bonds between atom pairs for applying a repulsive potential (default: 3).
`-msmolbar`	Sort out topological duplicates by molbar codes (activated by default—requires “molbar”).
`-msinchi`	Sort out topological duplicates by InChI codes (requires “obabel”).
`-msnfrag [int]`	Number of fragments printed by msreact (random selection).
`-msfragdist [real]`	Separate fragments before TS search from each other (default: 2.5 Å).
Special Options:
`-noKER`	Do not compute kinetic energy release (KER).
`-usetemp`	Use G_mRRHO contributions instead of only ZPVE (ZPVE is default).
`-scaleeinthdiss [real]`	Decrease the internal energy only for -H or -H2 abstractions (default: 0.5).
`-nsamples [int]`	Number of simulated runs in Monte Carlo (default: 10E05).
`-rrkm`	Compute rate constants via the RRKM equation instead of Eyring (default: Eyring).
`-sthr [int]`	RRHO cutoff for thermo contributions (default: 150 cm⁻¹).
`-ithr [int]`	Imaginary RRHO cutoff for thermo contributions (default: 100 cm⁻¹).
`-nthermosteps [int]`	Number of increments to compute thermal corrections for the IEE distribution (default: 200; take a multiple of 10).