How to set up frequency calculation with harmonic constrained potential

Yuezhi · October 29, 2024, 1:53am

On the Q-Chem manual, there is a sample job for geometry optimization with harmonic constrained potential applied on specific atoms: 9.4.7 Atomic Confining Potentials as Alternatives to Constrained Optimizationâ£ 9.4 Constrained Optimization â£ Chapter 9 Exploring Potential Energy Surfaces: Searches for Critical Points and Molecular Dynamics â£ Q-Chem 6.2 Userâs Manual

I wonder if one wants to perform a harmonic frequency calculation at the optimized structure, what would be the recommended way to set up the input. Should one simply read in the optimized structure, change the jobtype to freq and keep all the other settings unchanged? Is it needed to update the coordinates of the confined atoms under $coords?

paige.bowling · October 29, 2024, 3:51pm

Hello Yuezhi,

Below is a sample of how you could set up an input to complete a geometry optimization followed by a frequency calculation. You do not (and should not) change the coordinates in the “$coords” section between the two calculations.

$molecule
0 1
6 5.769900 -2.321232 4.072389
6 4.767069 -1.871617 3.005656
6 5.098441 -2.427805 1.616941
7 4.170381 -2.021473 0.544478
6 7.105935 -3.153945 -3.156034
6 6.491813 -2.652981 -1.864550
8 5.179075 -2.873690 -1.815239
8 7.135603 -2.116482 -0.976827
7 -1.588193 4.199762 -2.245353
6 -1.581097 5.082075 -3.395533
6 -8.865750 -1.562067 2.667196
7 -8.547199 -2.179029 1.390102
6 -7.278447 -2.225837 0.882184
7 -6.248145 -1.782039 1.588602
7 -7.078002 -2.753936 -0.322985
6 1.115307 5.142634 3.446943
6 1.667787 4.053650 2.556181
6 2.004402 4.302378 1.221306
6 1.841554 2.747373 3.037589
6 2.486355 3.291138 0.387444
6 2.319154 1.725483 2.222298
6 2.637277 1.997325 0.888494
8 3.103003 0.956591 0.120165
6 -1.353652 2.345154 0.158362
6 -1.672753 1.990278 -1.253894
6 -1.827970 2.846424 -2.406244
8 -2.200833 2.388893 -3.508889
7 -1.936449 0.691591 -1.556272
6 -1.895840 -0.407328 -0.828119
6 -2.441564 -1.701514 -1.335011
6 -3.794873 -2.047207 -0.667237
8 -4.694276 -2.524678 -1.407573
8 -3.873100 -1.813389 0.575888
6 1.312079 -1.012027 -1.427468
8 1.504964 -0.116299 -2.154358
8 1.141341 -1.918995 -0.709231
1 5.520154 -1.909719 5.055318
1 6.784913 -1.994564 3.821567
1 4.748571 -0.774081 2.956209
1 3.753606 -2.186659 3.292677
1 6.100009 -2.118553 1.302025
1 5.108070 -3.524367 1.648282
1 4.084949 -1.004914 0.519803
1 4.805935 -2.538974 -0.924604
1 3.232699 -2.376781 0.722947
1 6.955912 -4.234631 -3.241899
1 8.171291 -2.925572 -3.172639
1 -2.288132 4.686667 -4.124680
1 -1.032339 4.476446 -1.451029
1 -9.916933 -1.750319 2.890456
1 -8.270832 -2.017933 3.463972
1 -9.290572 -2.227570 0.710052
1 -5.236229 -1.838639 1.175748
1 -6.423311 -1.205084 2.395354
1 -7.824217 -3.265025 -0.767004
1 -6.101102 -2.710878 -0.773402
1 1.281440 6.133723 3.015260
1 1.582508 5.126882 4.437202
1 1.894098 5.306799 0.820221
1 1.595347 2.522950 4.072468
1 2.745111 3.510161 -0.645864
1 2.445657 0.716827 2.601837
1 3.149938 1.228552 -0.806761
1 -1.358357 3.425646 0.317828
1 -2.102992 1.919391 0.845027
1 -0.375022 1.969276 0.493667
1 -2.215187 0.634137 -2.547071
1 -1.640766 -0.310509 0.219050
1 -1.750518 -2.522893 -1.100232
1 -2.580625 -1.686751 -2.420159
1 -0.596734 5.147773 -3.882258
1 -1.890235 6.089306 -3.098428
1 -8.701526 -0.475564 2.674801
1 5.787885 -3.413069 4.164062
1 6.608807 -2.690698 -4.013518
1 0.035008 5.027369 3.598860
$end

$rem
method b3lyp
basis  6-31G(d,p)
jobtype opt
GEOM_OPT_COORDS 0
GEOM_OPT_MAX_CYCLES 1500
SYMMETRY             false
SYM_IGNORE           true
NO_REORIENT          true
HARM_OPT 1 ! turns on the harmonic confiner
HOATOMS 5 ! No. of constrained atoms
HARM_FORCE 450 !force constant
$end

$harmonic_opt
1 5 10 11 16 
$end

$coords
1 5.769900 -2.321232 4.072389
5 7.105935 -3.153945 -3.156034
10 -1.581097 5.082075 -3.395533
11 -8.865750 -1.562067 2.667196
16 1.115307 5.142634 3.446943
$end


@@@@

$molecule
read
$end

$rem
method b3lyp
basis  6-31G(d,p)
jobtype freq
SYMMETRY             false
SYM_IGNORE           true
NO_REORIENT          true
HARM_OPT 1 ! turns on the harmonic confiner
HOATOMS 5 ! No. of constrained atoms
HARM_FORCE 450 !force constant
$end

$harmonic_opt
1 5 10 11 16 
$end

$coords
1 5.769900 -2.321232 4.072389
5 7.105935 -3.153945 -3.156034
10 -1.581097 5.082075 -3.395533
11 -8.865750 -1.562067 2.667196
16 1.115307 5.142634 3.446943
$end

Let me know if you have any other questions,
Paige

Yuezhi · October 29, 2024, 6:46pm

Thank you, Paige! That is very helpful.

Best, Yuezhi