MSREACT Keywords

This page contains the documentation of available keywords for the MSREACT mode. Required arguments will be marked with < >, optional arguments are marked by brackets [ ].

Table of contents

MSREACT Keywords
MSREACT special settings specified in an input file

Note: Note that the MSREACT mode produces many topologically equivalent duplicates. To sort out duplicated structures you require the molbar program that can be obtained from the respective molbar GitHub repository (recommended option). Alternatively, you can use InChI keys generated by the obabel program openbabel GitHub repository . The programs have to be added to your path as molbar or obabel, respectively.

The MSREACT extension of CREST can be invoked via the command line. To activate MSREACT, use a command similar to

crest <INPUTFILE> -msreact [OPTIONS]

The input file coordinates have to be provided and can be in any format supported by CREST. The general and technical command line options of CREST also apply to the MSREACT runtype (see Keyword Documentation). Take care to always set the number of cores with --T <INT>. The [OPTIONS] that can be used in conjunction with -msreact are documented below.

MSREACT Keywords

Command	Description
`--msnbonds <int>`	maximum number of bonds between atoms pairs for applying a repulsive potential (default 3)
`--msnshifts <int>`	perform int optimizations with randomly shifted atom positions (default 0)
`--msnshifts2 <int>`	perform </i>int</i> optimizations with randomly shifted atom positions and a repulsive potential applied to atom pairs (default 0)
`---msnoattrh`	deactivate attractive potential between hydrogen atoms and LMO centers.
`--msmolbar`	sort out topological duplicates by molbar codes (requires sourced “molbar”)
`--msinchi`	sort out topological duplicates by InChI codes (requires sourced “obabel”)
`--mslargeprint`	do not remove temporary files and MSDIR with constrained optimizations and write directories for isomers and fragmentpairs, as well as seperated fragment structures in individual directories. The nomenclature of the directories is `p<number of product>` for isomers and product pairs. For fragments, it is `p<number of corresponding product pair>f<number of respective fragment>`.
`--chrg <int>`	set the molecules´ charge (default 0, for EI-MS: 1, for DEA-MS: -1).
`--ewin <real>`	set energy window in for sorting out fragments kcal/mol [default: 200.0 kcal/mol].
`--msiso`	print only non-dissociated structures (isomers).
`--msnoiso`	print only dissociated structures.
`--msinput <file>`	read advanced settings from input file.

MSREACT special settings specified in an input file

Additional [OPTIONS] can be changed in an additional input file which is read via -msinput <filename>. The specific keywords are documented below. One should use only one keyword <value> pair per line.

Command	Description
`fragdist <real>`	increase distance between fragments xyz structures (default 0 Angstrom). (Useful for input generation of automatic reaction pathfinder.)
`atomshift <real>`	shift of atoms in random atom displacement (default 0.75 Angstrom)
`distthr_attr <real>`	distance threshold in Angstrom for H-LMO attraction (default 4.0 Angstrom)
`fc_rep <real>`	force constant for repulsive potential between atom pairs (default 0.5)
`fc_attr <real>`	force constant for attractive potential between hydrogen and LMO centers (default -0.5)
`etemp <real>`	change electronic temperature in xTB optimizations (default 5000 K)