How to solve IRC oscillation and obtain IRC figure with mass-weighted coordinates?

Questions
#1

The input file command on TS calculation from the products and reactants is as follows:
$rem
JOBTYPE fsm
METHOD pbe0
DFT_D = D3_BJ
BASIS aug-cc-pVTZ
FSM_NGRAD 6
FSM_NNODE 20
FSM_MODE 2
FSM_OPT_MODE 2
SYMMETRY false
SYM_IGNORE true
$end

@@@

$molecule
read
$end

$rem
JOBTYPE ts
BASIS aug-cc-pVTZ
METHOD pbe0
DFT_D = D3_BJ
SCF_GUESS read
GEOM_OPT_HESSIAN read
MAX_SCF_CYCLES 25000000
GEOM_OPT_DMAX 50
GEOM_OPT_MAX_CYCLES 10000000
SYMMETRY false
SYM_IGNORE true
$end

@@@

$molecule
read
$end

$rem
JOBTYPE freq
BASIS aug-cc-pVTZ
METHOD pbe0
DFT_D = D3_BJ
SCF_GUESS read
$end

@@@

$molecule
read
$end

$rem
JOBTYPE rpath
BASIS aug-cc-pVTZ
METHOD pbe0
DFT_D = D3_BJ
SCF_GUESS read
RPATH_COORDS=0
RPATH_MAX_CYCLES 1000000
RPATH_MAX_STEPSIZE=10
RPATH_TOL_DISPLACEMENT=100000
RPATH_PRINT=10
$end

We have encountered a number of problems, as follows:

  1. the outfigure is oscillated, as follows:
    图片1
  2. where is mass-weighted coordinates ?in .out or where? watting for your help.
#2

(a) is this a different issue from this one:

(b) I can’t solve this issue without the input file (including molecular coordinates), and it would be helpful if you could provide a minimal basis (small basis and small molecule).

#3

Thank you very much for your patience and help, the input file was displayed , as follows:
$molecule
0 1
O 0.0038887696 -0.0102488494 0.0473750939
O -0.0038442878 -0.0111764720 3.8628084944
O 1.9071776921 0.0104817575 1.9590674296
O -1.9073001025 -0.0261823425 1.9510540344
H 0.7830889866 -0.0085279483 0.6486520261
H -0.7829356612 -0.0247796167 3.2615475436
H 1.3061082289 0.0091742108 2.7384555637
H -1.3064846453 -0.0145489194 1.1715878823
H 0.1044665570 0.7566117128 -0.5178398149
H -0.1176673445 0.7558790502 4.4252617882
H 2.4793923263 -0.7504277425 2.0650991913
H -2.4648314094 -0.7977040104 1.8434595876

O -0.9511249722 -0.3795538207 -0.1216620894
O 0.4055041397 0.1164225647 4.8049620219
O -2.2252030040 -0.7540516343 4.7605558746
O -1.0683941537 0.5935126158 2.5700078854
H -0.0741199871 -0.3587986445 -0.5098634599
H 0.1314416081 0.3535548544 3.8953872408
H -1.3112823208 -0.5521796168 5.0350727701
H -1.0430516170 0.1930629667 1.6896256299
H -1.4894473902 0.1875626621 -0.6778103909
H 1.1318206388 -0.5008015494 4.7112093835
H -2.7884257761 -0.2798604108 5.3735785750
H -1.7359479620 0.1090099721 3.0811834466
$end

$rem
JOBTYPE fsm
METHOD pbe0
DFT_D = D3_BJ
BASIS aug-cc-pVTZ
FSM_NGRAD 6
FSM_NNODE 20
FSM_MODE 2
FSM_OPT_MODE 2
SYMMETRY false
SYM_IGNORE true
$end

@@@

$molecule
read
$end

$rem
JOBTYPE ts
BASIS aug-cc-pVTZ
METHOD pbe0
DFT_D = D3_BJ
SCF_GUESS read
GEOM_OPT_HESSIAN read
MAX_SCF_CYCLES 25000000
GEOM_OPT_DMAX 50
GEOM_OPT_MAX_CYCLES 10000000000
SYMMETRY false
SYM_IGNORE true
$end

@@@

$molecule
read
$end

$rem
JOBTYPE freq
BASIS aug-cc-pVTZ
METHOD pbe0
DFT_D = D3_BJ
SCF_GUESS read
$end

@@@

$molecule
read
$end

$rem
JOBTYPE rpath
BASIS aug-cc-pVTZ
METHOD pbe0
DFT_D = D3_BJ
SCF_GUESS read
RPATH_COORDS=0
RPATH_MAX_CYCLES 50
RPATH_MAX_STEPSIZE=10
RPATH_TOL_DISPLACEMENT=100000
$end
Based on this, we calculated the transition state and its intrinsic reaction coordinate. The IQmol figure is as follow:

捕获
捕获849×405 17.4 KB

In short, there are some questions that require your help.
1.We want to obtain the mass-wighted IRC figure, and we want to know where to get the mass-wighted IRC coordinates? in .out or Vfile.txt or others? In the second column of Vfile.txt, does the value from 0 to 6.51448 refer to the mass-weighted coordinate?
图片1
图片1541×563 11.1 KB

2.The current IRC figure displayed in IQMOL seems to be via the FSM method, not the standard IRC, how do I get the IRC figure from the IRC and rpath commands?

waitting for your helpful response.

#4

I don’t think that you want to run this as a sequence of compound jobs. Run them one at a time and pay attention to the output at each step. Run the FSM job, go to stringfile.txt and find the highest-energy structure, use that as your guess for the subsequent TS search. Confirm the TS with a frequency calculation. Then do the IRC search.

#5

Okay, thanks teacher, I’ll try to calculate it.

#6

We have carried out an IRC search in the last step according to your suggestion.The input file is as follows:

捕获
捕获597×841 11 KB

The output file is as follows:
1
2
2890×863 16.7 KB

How to obtain IRC figure?in .out ?And how to obtain mass-weighted IRC figure?

#7

Based on the SCF energy that you are showing me, and comparing to the list of energies from Vfile.txt, this structure is almost certainly not the TS. Did you check it with a frequency calculation?

In recent versions of Q-Chem, a successful IRC calculation will print the sequence of geometries that comprise the path at the end, with a heading

 ============================================
      FORWARD RXN PATH (direction = +1)
 ============================================
#8

Thank you for your help. We are seeking the activation of Q-Chem 6.0.2.

#9

Great. I just checked an the cleanup of the IRC output was indeed released only with 6.0.2. (That capability with IQmol is still pending but once you have the structures from the Q-Chem output, they can be visualized in a variety of ways.)