Create GSM jobs

In this procedure, Dandelion generates possible GSM jobs or seeds, from each optimized mother structure. The overall algorithm calculates the number of bonds to be broken or added, determines possible reactions, and generates all viable driving coordinates. You can verify that all possible GSM jobs are generated from your optimized mother structures.

  ├── ClGeom-m7138-i1-c1-opt
  │   ├── gsm0000
  │   ├── gsm0001
  │   ├── gsm0002
  ...
  ├── ClGeom-m7164-i1-c1-opt
  │   ├── gsm0000
  │   ├── gsm0001
  │   ├── gsm0002
  ...

Each GSM job is organized into a directory containing three files:

File	Description
gsm.sh	A Bash script that initiates the GSM calculation process.
params.log	A log file detailing the parameters used and the connection limits applied.
ISOMERS.txt	Contains information on bond breaking and formation in the calculated reactions.

params.log

Connection limits:
  H: 1, 1
  C: 2, 4
  N: 1, 3
  O: 1, 2
  F: 1, 1
  S: 1, 2
  CL: 1, 1
  BR: 1, 1
maxbreak = 2
maxform = 2
maxchange = 3
single_change = False
equiv_Hs = False
minbreak = 0
minform = 0
minchange = 1

Parameter	Description	Default
Connection Limits	Minimum and maximum bonds allowed for each atom.
maxbreak	Maximum number of bonds that can be broken in a reaction.	2
maxform	Maximum number of bonds that can be formed in a reaction.	2
maxchange	Maximum number of total bond changes allowed in a reaction.	3
single_change	Consider single bond changes (e.g., nbreak=1, nform=0) or not.	False
equiv_Hs	Treat equivalent hydrogen atoms as unique or not.	False
minbreak	Minimum number of bonds that can be broken in a reaction.	0
minform	Minimum number of bonds that can be formed in a reaction.	0
minchange	Minimum number of total bond changes allowed in a reaction.	1

ISOMERS.TXT

  BREAK 5 6
  ADD 4 6
  ADD 3 6