The hess Section of the Jaguar Input File

  • Overview
  • Examples

If an input file has a non-empty hess section, the keyword inhess in the gen section is set to 2 automatically, and a Hessian is read in from the hess section. Since for a Hessian H, Hij = Hji, only the elements with j ≤ i are read in, and the program symmetrizes the matrix itself later.

Since the Hessian has dimensions of 3N×3N, where N is the number of atoms (including dummy atoms), it may be large, so files listing all elements in each row by order of rows could be unwieldy and difficult to read. Therefore, the Hessian is assumed to be presented in blocks composed of five columns each (with the last block possibly having fewer than five columns, if 3N is not a multiple of five). The format used for the hess section is the same as that used in Gaussian files or BIOGRAF (.hes) files. All Hessian elements for dummy atoms should be set to 0 (as they are in Jaguar output).

Each set of elements from a block of five columns should be preceded by a line containing one or more arbitrary integer labels; for instance, column labels could be convenient for keeping track of the elements when looking at the hess section. All of the elements within a five-column block for which j (the column indicator) is less than or equal to i (the row indicator) are then read in, one row at a time. Each row of five or fewer matrix elements starts with an arbitrary integer label; this integer is not used in the program, but can be used to label the row, for example. When the relevant matrix elements from that entire five-column block have been read in, the next block is read in the same way, until all of the matrix elements for the lower triangle of the matrix have been entered.

For example, in the unlikely event that you wanted to enter this Hessian:

11

21

31

41

51

61

71

81

21

22

32

42

52

62

72

82

31

32

33

43

53

63

73

83

41

42

43

44

54

64

74

84

51

52

53

54

55

65

75

85

61

62

63

64

65

66

76

86

71

72

73

74

75

76

77

87

81

82

83

84

85

86

87

88

you would need to enter the elements from the bottom triangle of the Hessian (shown in bold above) in the following way:

&hess
1
1     11
2     21     22     
3     31     32     33     
4     41     42     43     44     
5     51     52     53     54     55     
6     61     62     63     64     65     
7     71     72     73     74     75     
8     81     82     83     84     85     
6
6     66     
7     76     77     
8     86     87     88     
&

Here the beginning of a block is marked with the index of the first column of the Hessian, and the rows in the block have the row number as the first value. This practice helps you to identify the Hessian matrix elements, though as mentioned above, you can have arbitrary integer values in the label (first) column of the input.

Geometry Optimization Examples

Note: No inhess keyword value is set. It is not required if a Hessian is supplied directly. A useful trick for geometry optimization is to use initial Hessians from cheap levels of theory.

Example input file (opt-inhess-0002.in):

&gen
igeopt=1
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
O1   0.0000000000      0.0000000000     -0.0667079824
H2   0.0000000000      0.7594973815      0.5293520449
H3   0.0000000000     -0.7594973815      0.5293520449
&
&hess
   1
   1 -1.641347E-03
   2  2.150504E-08  6.695321E-01
   3 -2.439959E-08 -4.572074E-08  4.569404E-01
   4  7.121612E-04  1.556816E-09  5.527648E-08 -5.033506E-04
   5 -2.129897E-08 -3.347701E-01 -1.983446E-01 -7.675571E-09  3.666220E-01
   6 -5.709321E-09 -2.627293E-01 -2.284449E-01  4.002528E-09  2.305369E-01
   7  7.120857E-04 -2.684376E-08  2.863546E-08 -2.061418E-04  6.976638E-09
   8  3.451838E-09 -3.347701E-01  1.983445E-01  1.125676E-08 -3.184840E-02
   9 -4.688897E-09  2.627294E-01 -2.284449E-01 -4.207454E-08 -3.219406E-02
   6
   6  2.173661E-01
   7  9.941169E-10 -5.033291E-04
   8  3.219410E-02  8.780421E-09  3.666219E-01
   9  1.108658E-02  1.497606E-09 -2.305369E-01  2.173660E-01
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_inhess_0002 opt-inhess-0002.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt-inhess-0002.in
Output files

Transition State Geometry Optimization Examples

Note: To get the other side of the reaction path, set ircmode=backward. One could also get the whole path in one job with ircmode=both, but this is inefficient. The transition state should be optimized at the same level of theory as used for the IRC.

Example input file (opt_ts-irc-0001.in):

&gen
irc=1
ircmode=forward
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
C1            0.0692136180      0.2132816644     -0.3879323240 
C2            1.4720844665      0.2296330313      0.1734604239 
O3            2.2428204464      1.1677738906      0.1309430510 
N4            2.1499220058     -1.2437703044      0.0898551824 
C5            3.5627058603     -1.2437951941     -0.3080475774 
H6            4.0343246067     -2.1845128465     -0.0147401167 
H7           -0.4855722193     -0.6754858693     -0.0829860366 
H8           -0.4514113750      1.0974920377     -0.0186382961 
H9            0.1210183915      0.2689320396     -1.4813556128 
H10           1.5855338582     -1.8961919808     -0.4512488016 
H11           3.6665480964     -1.1009168850     -1.3871598360 
H12           4.0480965526     -0.4072652266      0.1955270219 
O13           1.0996672074     -0.3560287728      1.9259912398 
H14           1.8663029436     -1.2303195726      1.2206894514 
H15           1.6407504151      0.2556717461      2.4468241668 
&
&hess
   1
   1  4.985984E-01
   2  1.022192E-02  6.036747E-01
   3 -4.467415E-02 -1.042631E-03  5.443946E-01
   4 -1.847519E-01 -1.236992E-03 -4.896982E-02  7.032186E-01
   5  3.569906E-03 -7.889063E-02  5.341051E-04  3.093762E-01  5.805400E-01
   6 -4.414289E-02  3.075284E-03 -8.099072E-02  1.068053E-01 -1.445122E-02
   7 -2.638700E-02 -3.841405E-02  1.186097E-03 -3.696389E-01 -2.930791E-01
   8 -1.579608E-02 -1.203816E-03  3.307070E-04 -3.135045E-01 -4.418800E-01
   9 -9.846858E-03 -1.116586E-02  1.272042E-02  4.209255E-03  1.031146E-02
  10 -1.256079E-02  2.837095E-02  6.328622E-03 -9.420234E-02 -2.760635E-02
  11  8.074277E-03 -8.180085E-03 -4.246788E-03 -1.403619E-02 -2.511348E-03
  12 -6.141829E-03  8.876670E-03  9.186548E-03  6.449519E-03 -6.634393E-03
  13  1.131178E-03 -4.200063E-04 -1.016255E-05 -1.510764E-02  2.598603E-02
  14  1.070207E-03 -4.879721E-03 -1.405763E-03  2.782561E-02  1.109159E-02
  15 -1.655723E-03  2.936403E-03  1.590250E-03 -3.800617E-03 -5.299978E-03
  16 -5.901058E-04  2.125121E-03  8.436201E-04 -4.377328E-03 -1.041980E-02
  17 -3.846097E-05  1.373446E-04 -5.110873E-05 -1.966200E-03 -1.326630E-03
  18  1.237235E-04 -6.688404E-04 -3.383283E-04  1.998806E-03  9.666394E-04
  19 -1.173074E-01 -1.094637E-01  3.812270E-02 -1.150648E-02 -3.048214E-02
  20 -1.130304E-01 -2.317935E-01  6.339941E-02  1.986910E-03 -2.210707E-03
  21  4.106264E-02  6.657354E-02 -6.890803E-02 -4.891653E-03 -1.331228E-02
  22 -1.084907E-01  1.054392E-01  4.532612E-02 -1.429915E-02  2.798514E-02
  23  1.080574E-01 -2.318369E-01 -7.814281E-02  1.958646E-04 -1.413140E-03
  24  4.718613E-02 -7.944934E-02 -7.820947E-02 -6.806352E-03  1.139206E-02
  25 -5.024001E-02 -1.452310E-03  1.352202E-02  2.649424E-03  5.370487E-05
  26 -1.826418E-03 -4.918181E-02  1.368002E-02  3.639358E-04 -2.231746E-03
  27  1.452739E-02  1.321935E-02 -3.075969E-01  3.084118E-03  4.864820E-04
  28 -2.538287E-04  1.656919E-03 -3.835681E-04  1.146800E-02 -5.379098E-04
  29 -2.614891E-04  1.640485E-03  1.317667E-03 -2.194747E-02 -5.552470E-03
  30 -5.123418E-04 -7.816618E-04  9.256446E-04  4.276077E-03  2.772825E-03
  31  1.135445E-04 -1.452176E-04 -8.656111E-05  2.617790E-04 -3.392604E-03
  32 -1.812774E-05  4.009060E-05 -2.733422E-05 -2.768754E-06  1.079156E-03
  33  1.734414E-04 -2.531512E-04 -1.627890E-04  2.129085E-04  2.837961E-03
  34  1.355931E-04  5.585949E-04  1.242287E-04 -3.382290E-03 -6.716188E-03
  35 -4.872590E-04 -5.381049E-04  8.740019E-05  2.386577E-03  1.169051E-03
  36 -5.601811E-05  5.784216E-05  3.629654E-05 -4.393252E-04 -2.036535E-03
  37  2.436439E-03  9.573235E-04 -1.428457E-02 -4.082285E-02  5.078931E-03
  38 -1.454727E-03  2.951483E-03  6.410734E-03  5.713458E-03 -4.965616E-02
  39  1.897772E-04  1.530101E-03 -2.357119E-02 -1.434384E-02 -2.050847E-02
  40 -1.955888E-03  2.486889E-03  3.253569E-03  1.837701E-02 -2.956220E-03
  41  2.542492E-03 -1.906310E-03 -3.832832E-03 -4.464500E-03 -1.733952E-02
  42  2.717630E-03 -3.728952E-03 -5.891615E-03 -3.269098E-02  4.798331E-02
  43  8.508411E-05 -7.230364E-04 -2.827313E-04  2.127656E-03  3.123252E-03
  44 -6.330762E-04 -4.139792E-05  2.982404E-03  9.251580E-03  9.058447E-03
  45  1.022238E-03  7.803387E-04 -3.140184E-03 -1.500650E-02 -1.504003E-02
   6
   6  1.891258E-01
   7 -1.215664E-02  3.788865E-01
   8 -5.477972E-03  3.522318E-01  5.287214E-01
   9 -7.781747E-02 -9.765378E-03 -1.866249E-02  5.855060E-02
  10 -9.889992E-03  2.396759E-02 -1.220042E-02 -2.326645E-03  5.719330E-01
  11  2.818519E-02 -1.309695E-02 -6.810470E-02 -4.378007E-03  1.426693E-01
  12 -7.674009E-02 -5.391740E-03 -4.888372E-03  1.843096E-02  2.138924E-02
  13  4.070270E-03 -7.033202E-03 -8.498340E-03 -5.190194E-05 -1.995417E-01
  14 -2.840603E-03 -4.900019E-04 -1.944517E-03  1.739582E-04 -1.953501E-03
  15 -3.667065E-03  7.420796E-04  8.735631E-04  6.980367E-04  4.548669E-02
  16 -1.372223E-03  3.643146E-03  1.342802E-03 -5.934102E-04 -2.550442E-02
  17  5.098645E-04  2.126253E-03  8.719094E-04 -4.502895E-04 -1.889224E-03
  18  8.865701E-04 -8.116343E-05 -7.626028E-05  1.420408E-05  5.665637E-03
  19  1.334386E-02 -6.906796E-03  8.975771E-04 -4.252507E-03  4.914523E-04
  20 -1.590831E-04 -6.971463E-05  2.612244E-03  2.964627E-04  6.419663E-04
  21  2.834154E-03 -4.398264E-03  2.520566E-04  6.041701E-05  4.262514E-04
  22  1.165565E-02  3.241029E-03 -2.258676E-03 -1.202332E-03 -5.242114E-03
  23  1.894415E-04 -8.590803E-04  6.960479E-04  5.511079E-05  3.822324E-04
  24  3.123534E-03  1.491534E-03  2.781627E-04 -2.725460E-04 -3.734763E-03
  25 -3.100032E-02  3.254835E-04  1.023198E-03  3.133684E-03  1.965670E-04
  26  4.697291E-04 -6.581400E-04 -1.149472E-05  3.887231E-04  1.011431E-05
  27 -1.364797E-02 -4.418780E-04 -4.524588E-05  2.314014E-03 -9.033280E-04
  28  5.710707E-03 -1.280890E-04  4.775850E-03 -7.659709E-04 -1.680027E-01
  29 -1.139323E-02  2.806879E-03 -7.685155E-03  1.095925E-03 -1.329562E-01
  30 -6.854407E-04 -1.024416E-04  3.779371E-03  1.886351E-04 -1.162827E-01
  31  2.005472E-03  1.167707E-03  1.322100E-03 -4.103378E-04 -1.358718E-02
  32 -9.255338E-04 -2.058354E-04 -3.552785E-04  1.073493E-03 -6.075124E-04
  33 -8.086579E-04 -8.561612E-04 -1.341512E-03  9.668297E-04  6.813461E-03
  34 -3.866991E-04  3.057775E-03  2.934189E-03  5.583282E-04 -2.477499E-02
  35 -1.363596E-03  1.423101E-03 -3.203031E-03 -1.841376E-04 -2.856143E-03
  36  1.493745E-03  1.712722E-03  1.266629E-04 -1.558178E-03  4.547418E-03
  37 -1.066942E-02  2.756671E-03 -1.106440E-02  1.586406E-02  5.746055E-03
  38 -5.113982E-02 -1.461452E-02 -6.799558E-03  3.087400E-02  2.723057E-02
  39  2.658720E-02  1.815501E-02  2.549021E-02 -9.742119E-03  3.245907E-02
  40 -3.407957E-02 -5.241110E-03  3.237273E-05  5.511014E-03 -5.204521E-02
  41  5.638038E-02  5.203961E-03  1.823917E-03 -8.136735E-03 -2.373028E-02
  42  3.955872E-02  7.390720E-03 -2.579613E-03 -1.055272E-02  5.094914E-03
  43  1.073796E-04 -1.665955E-03 -1.197846E-03  4.358715E-05 -6.852459E-03
  44 -1.017638E-03 -2.251491E-03 -3.495117E-03 -1.321005E-03  4.559514E-03
  45 -9.228660E-03  2.543520E-03  1.939123E-03  5.953171E-03  4.991874E-03
  11
  11  3.932701E-01
  12  1.652254E-01  4.548462E-01
  13 -1.556924E-02  2.117681E-02  4.767899E-01
  14 -9.592103E-02 -8.244157E-03 -6.277825E-03  6.123560E-01
  15 -1.121731E-03 -9.962233E-02  3.212088E-02  6.427710E-03  5.893896E-01
  16  3.498163E-02 -3.645947E-03 -9.065957E-02  9.250206E-02 -3.051712E-02
  17  5.166576E-03 -2.017184E-03  9.761012E-02 -2.537313E-01  6.461120E-02
  18 -1.188736E-02  3.252549E-03 -3.225406E-02  6.780039E-02 -7.309024E-02
  19  1.769291E-03 -2.240635E-04  1.492180E-04 -5.858783E-05  2.770632E-04
  20  1.054983E-04 -7.634075E-04 -3.098770E-04  2.759028E-04  7.940260E-05
  21  2.669748E-04 -3.258095E-04  5.439370E-05 -2.208976E-04 -1.375190E-04
  22  5.028378E-04 -2.916702E-03  2.255912E-04  1.434528E-03 -8.016156E-04
  23  1.003535E-03  5.381508E-05 -1.319391E-04 -1.664722E-04  3.565396E-04
  24  1.070795E-03 -1.297097E-04 -3.301659E-05  9.252162E-04 -6.061892E-04
  25 -2.946594E-04  2.542660E-03  1.358490E-05  8.268202E-05  8.034601E-05
  26  1.874002E-04 -5.698551E-04  2.465401E-05 -7.629418E-05 -1.287487E-04
  27  1.770528E-04  2.002433E-03  4.092991E-05  2.354675E-04 -4.579702E-05
  28 -1.247799E-01 -1.031803E-01 -1.630067E-02 -2.306804E-02 -2.004172E-02
  29 -1.964463E-01 -1.325790E-01  4.878414E-03  3.082449E-03  1.988089E-03
  30 -1.421179E-01 -1.569486E-01  9.117665E-03  9.934487E-03  6.346716E-03
  31 -4.178662E-03  4.379810E-02 -5.012478E-02 -1.222554E-03  1.013150E-02
  32  7.420825E-04 -6.740050E-04 -1.734963E-03 -5.636709E-02  3.455484E-02
  33 -4.074989E-04 -5.749680E-03  1.709728E-02  3.394346E-02 -3.117748E-01
  34 -2.708786E-02 -1.563336E-02 -9.808763E-02 -8.692238E-02 -5.259622E-02
  35  2.467071E-03  1.883205E-03 -9.649032E-02 -2.118278E-01 -1.009351E-01
  36  1.022426E-02  6.514031E-03 -5.859540E-02 -1.011931E-01 -1.141312E-01
  37  2.019490E-02  5.136301E-02  4.424459E-03 -8.919199E-04 -1.616828E-04
  38  5.127094E-03 -6.180091E-02 -5.483989E-03  1.197293E-03 -6.910807E-03
  39 -2.990125E-02 -5.190536E-02 -3.770037E-03 -1.309653E-03 -5.549287E-03
  40 -9.471339E-03 -1.659741E-02 -6.025108E-03 -2.361953E-03  1.910023E-02
  41 -3.792448E-02  4.577650E-02  6.855361E-03 -3.560017E-03  3.809640E-03
  42 -1.048307E-02 -1.017400E-01  1.082948E-02 -3.707784E-03  1.183190E-02
  43  3.373073E-04  7.055651E-03  2.234615E-04  3.067496E-04  1.605956E-03
  44  1.008981E-03 -3.680737E-03 -4.426161E-04  4.441281E-04 -1.208449E-03
  45 -6.154931E-04 -1.147187E-03  1.772656E-04 -4.999787E-04 -1.235412E-03
  16
  16  1.075992E-01
  17 -1.070166E-01  2.684403E-01
  18  3.016255E-02 -7.089293E-02  7.110972E-02
  19  1.418016E-04  1.909962E-05 -2.150361E-05  1.268958E-01
  20 -2.797843E-05  2.604594E-05  4.040160E-05  1.213239E-01  2.478250E-01
  21  5.227808E-05  2.770226E-05  2.173845E-05 -4.164134E-02 -7.039853E-02
  22 -6.130178E-04 -2.755726E-05  2.187754E-04  9.355780E-03 -1.405384E-02
  23  9.939420E-05  6.664764E-05 -7.363411E-06  1.284335E-02 -1.870518E-02
  24 -3.825313E-04  1.733181E-05  1.127314E-04 -5.652362E-03  8.034981E-03
  25  1.884628E-05 -1.468898E-06  4.274247E-05 -9.005034E-04  1.572579E-03
  26  7.787341E-08  1.646921E-05 -3.428845E-06  8.624670E-04  5.596892E-04
  27 -6.342751E-05 -2.993512E-06  3.976158E-05  1.087070E-04 -6.106426E-04
  28 -3.176739E-04  4.731388E-04 -4.897923E-04 -1.590919E-03  5.246652E-04
  29  2.903784E-04  6.148007E-05  2.822240E-04  1.259631E-03  2.403863E-04
  30 -6.196470E-04 -2.566991E-04 -2.349741E-06  5.014511E-04  1.440014E-04
  31  1.784206E-03 -1.019820E-04 -1.345455E-02  6.851997E-05  8.642558E-06
  32 -2.235923E-03 -1.901817E-03  2.825521E-02 -4.559269E-05 -1.552044E-05
  33 -5.501677E-04 -1.144464E-04 -6.556511E-03 -5.339664E-05  9.683820E-07
  34  7.927221E-03  1.038772E-02  8.104638E-03  3.307318E-04  1.226459E-04
  35 -1.168530E-02 -1.771877E-02 -1.326967E-02 -2.866873E-04  6.861106E-05
  36  6.086662E-03  8.597933E-03  5.079666E-03 -2.609755E-05  5.693284E-05
  37 -1.067612E-04  2.033685E-04 -1.640549E-04  7.905363E-04  1.120191E-03
  38 -7.100420E-06 -1.241439E-04  4.393433E-04  1.556122E-03  1.079212E-03
  39  6.737798E-04 -5.661613E-04 -4.713464E-04 -6.847797E-04 -5.324952E-04
  40  1.092119E-03  1.917843E-04  1.270631E-04 -4.314129E-04 -1.414907E-04
  41  1.170476E-04  8.160579E-05 -9.803293E-04 -1.768751E-04  3.376626E-05
  42 -6.716504E-05  4.848445E-04 -7.297572E-05 -3.449237E-04  1.905529E-04
  43 -3.449908E-05  3.662602E-05  2.463782E-05  4.436057E-04  3.549487E-04
  44 -6.806719E-05 -6.466007E-05 -4.080512E-06 -1.761206E-05 -9.826663E-05
  45 -4.057671E-06  9.670880E-05  1.620943E-05  5.843616E-04  2.636593E-04
  21
  21  7.084206E-02
  22 -6.802053E-03  1.166318E-01
  23 -9.027352E-03 -1.168997E-01  2.461293E-01
  24  2.712649E-03 -4.804512E-02  8.523205E-02  8.131038E-02
  25  1.612735E-02 -7.471322E-04 -2.550863E-03  1.556577E-02  4.976099E-02
  26  2.607209E-02 -1.757125E-04  3.002162E-03 -2.651102E-02  8.088077E-04
  27 -6.137251E-03  1.482188E-04  1.451963E-03 -9.323726E-03 -1.425659E-02
  28  4.918087E-04 -2.069955E-04 -4.301813E-04 -3.070037E-05 -9.151932E-05
  29 -3.323884E-04 -5.794746E-04  6.056002E-04 -2.233866E-04  4.493986E-04
  30  1.020200E-04  1.922663E-04  1.590578E-04 -2.168984E-04  4.145534E-06
  31  1.151370E-05  2.387484E-05 -1.092654E-05 -3.400492E-05 -1.441239E-04
  32  3.339002E-05 -3.864463E-05 -1.941527E-05 -7.077499E-06  3.578851E-05
  33  1.101718E-05  8.004633E-05 -2.894326E-05  4.541160E-05  5.963509E-05
  34  1.493342E-05 -8.057138E-05  1.176920E-04 -3.401678E-05  8.050898E-05
  35 -8.120052E-05  6.417058E-05 -9.709983E-07  2.283781E-05 -3.794701E-05
  36  3.078137E-05 -5.455369E-06 -7.459942E-06  1.753289E-05  1.402053E-05
  37 -2.308452E-04  1.322235E-03 -1.086106E-03  8.344684E-04 -2.026223E-03
  38 -3.601565E-04 -2.373268E-03  1.076191E-03 -1.089129E-03  8.332152E-04
  39 -1.747924E-03  4.112410E-04  6.057099E-04  2.329377E-04 -3.849488E-03
  40 -5.457913E-04 -9.666260E-04  2.016678E-04 -1.907185E-04  1.071373E-03
  41  3.033270E-04  8.585903E-04 -4.216932E-04  2.534718E-04 -1.468491E-03
  42  6.385082E-04  1.928871E-03 -9.543450E-04  1.194677E-03 -1.371073E-03
  43  2.690804E-04 -1.464908E-04  6.568445E-05 -1.339642E-04  4.309044E-05
  44  2.029894E-04  1.191700E-04 -7.605648E-06  5.047541E-05  9.482964E-04
  45  6.617638E-06 -1.815225E-04  5.759636E-05  1.096916E-05 -6.096135E-04
  26
  26  4.647496E-02
  27 -1.520900E-02  3.348778E-01
  28  3.705613E-05 -9.735934E-05  1.799337E-01
  29 -3.948055E-04  4.368426E-04  1.374420E-01  2.019524E-01
  30  3.316152E-04 -3.593068E-04  1.128006E-01  1.418798E-01  1.533453E-01
  31  7.412041E-05 -1.814099E-04  1.501233E-03 -6.619068E-05  2.618818E-04
  32  2.132794E-05  1.399465E-05 -2.608747E-04 -2.758973E-05  8.706471E-04
  33 -2.204672E-05  4.447182E-05  6.050874E-04 -2.191762E-04  8.559955E-04
  34 -2.758119E-05  3.727888E-05 -6.208251E-03  1.044480E-03  2.837404E-03
  35 -1.586116E-06 -1.553492E-05  1.580593E-03 -4.651862E-04  7.125004E-04
  36  2.305705E-06 -6.225054E-06  2.583567E-03 -2.678296E-04  6.908384E-05
  37  7.253214E-04 -2.806103E-03 -3.790065E-03 -2.089409E-04  8.028176E-03
  38  1.744091E-03  8.960351E-05  2.949641E-04  2.182384E-03 -2.909722E-03
  39  7.389532E-04 -4.903622E-05  3.381858E-03 -2.033013E-03 -3.199405E-03
  40 -5.732334E-04  1.030120E-03  3.880135E-03  7.633651E-03 -2.016076E-02
  41  3.764893E-04 -9.026863E-04  2.498825E-03  9.670412E-04 -1.524159E-02
  42  2.041696E-04 -1.642086E-03 -8.972752E-05 -1.634360E-04 -5.927559E-04
  43  3.620831E-04 -2.274561E-04  1.151538E-04  2.182054E-04 -3.459445E-04
  44 -4.792174E-04  6.808451E-04 -2.154003E-04 -1.544890E-04  7.222227E-04
  45  5.653608E-04 -4.808099E-04 -4.975019E-04  2.109566E-04  1.775205E-04
  31
  31  6.033084E-02
  32  2.627628E-03  5.121953E-02
  33 -2.383043E-02 -3.802609E-02  3.338761E-01
  34  1.952740E-03  2.553888E-03  4.783205E-04  1.183110E-01
  35  3.934925E-03  5.423986E-03  3.466954E-03  1.032753E-01  2.247849E-01
  36 -1.391844E-02 -2.498239E-02 -1.338911E-02  5.819228E-02  1.086569E-01
  37 -1.263882E-03 -1.479128E-04  3.334609E-04  1.675174E-05 -2.684526E-06
  38  3.896823E-03 -1.447230E-05 -1.317196E-03  1.190661E-03 -8.042051E-04
  39  2.372182E-03  1.465592E-04 -6.218236E-04 -5.707047E-04  9.574717E-04
  40 -1.454351E-03  1.735561E-04 -7.050432E-04  8.852110E-04 -7.469779E-04
  41 -3.247798E-03  1.351053E-04  1.500980E-03 -1.614742E-03  4.940132E-04
  42 -6.976245E-03 -2.837144E-04  3.292562E-03 -1.430189E-03  1.817977E-04
  43 -6.267468E-04 -8.645682E-05  1.513497E-04 -1.457447E-04 -5.908799E-05
  44  5.023319E-04  3.822368E-05 -3.344543E-05  1.718977E-04  1.384160E-04
  45  3.112351E-04 -2.276136E-05 -2.803434E-05  2.977890E-04 -1.284507E-04
  36
  36  1.162906E-01
  37 -6.326879E-04  2.325917E-01
  38  3.463852E-04  1.730041E-01  2.702908E-01
  39 -3.255435E-04  1.216728E-01  2.033675E-01  2.413789E-01
  40  3.170309E-04 -3.074214E-02 -6.647616E-03  1.344136E-03  6.357577E-02
  41  5.145588E-04 -1.287865E-02 -3.733365E-03 -9.676562E-03  2.646651E-02
  42 -3.825672E-05 -2.785311E-02  4.176285E-02 -1.626648E-02  4.401337E-02
  43  2.216563E-04 -1.713310E-01 -1.831696E-01 -1.573437E-01  9.979555E-03
  44 -1.006902E-04 -1.750219E-01 -2.244648E-01 -1.682154E-01 -1.428958E-02
  45 -8.076661E-05 -1.412104E-01 -1.576788E-01 -1.548879E-01 -2.413239E-03
  41
  41  6.428960E-02
  42 -6.887696E-02  8.438787E-02
  43  3.043791E-03 -1.150293E-03  1.677703E-01
  44 -3.318060E-03 -2.087719E-05  1.773877E-01  2.214424E-01
  45 -8.924798E-04 -4.119387E-03  1.499941E-01  1.709621E-01  1.681916E-01
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_ts_irc_0001 opt_ts-irc-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_ts-irc-0001.in
Output files

Note: To get the other side of the reaction path, set ircmode=backward. One could also get the whole path in one job with ircmode=both, but this is inefficient. The transition state should be optimized at the same level of theory as used for the IRC.

Example input file (opt_ts-irc-0002.in):

&gen
irc=1
ircmode=forward       
ircmax=8             
ircmxcyc=30           
ircstep=0.1           
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
C1            0.0692136180      0.2132816644     -0.3879323240 
C2            1.4720844665      0.2296330313      0.1734604239 
O3            2.2428204464      1.1677738906      0.1309430510 
N4            2.1499220058     -1.2437703044      0.0898551824 
C5            3.5627058603     -1.2437951941     -0.3080475774 
H6            4.0343246067     -2.1845128465     -0.0147401167 
H7           -0.4855722193     -0.6754858693     -0.0829860366 
H8           -0.4514113750      1.0974920377     -0.0186382961 
H9            0.1210183915      0.2689320396     -1.4813556128 
H10           1.5855338582     -1.8961919808     -0.4512488016 
H11           3.6665480964     -1.1009168850     -1.3871598360 
H12           4.0480965526     -0.4072652266      0.1955270219 
O13           1.0996672074     -0.3560287728      1.9259912398 
H14           1.8663029436     -1.2303195726      1.2206894514 
H15           1.6407504151      0.2556717461      2.4468241668 
&
&hess
   1
   1  4.985984E-01
   2  1.022192E-02  6.036747E-01
   3 -4.467415E-02 -1.042631E-03  5.443946E-01
   4 -1.847519E-01 -1.236992E-03 -4.896982E-02  7.032186E-01
   5  3.569906E-03 -7.889063E-02  5.341051E-04  3.093762E-01  5.805400E-01
   6 -4.414289E-02  3.075284E-03 -8.099072E-02  1.068053E-01 -1.445122E-02
   7 -2.638700E-02 -3.841405E-02  1.186097E-03 -3.696389E-01 -2.930791E-01
   8 -1.579608E-02 -1.203816E-03  3.307070E-04 -3.135045E-01 -4.418800E-01
   9 -9.846858E-03 -1.116586E-02  1.272042E-02  4.209255E-03  1.031146E-02
  10 -1.256079E-02  2.837095E-02  6.328622E-03 -9.420234E-02 -2.760635E-02
  11  8.074277E-03 -8.180085E-03 -4.246788E-03 -1.403619E-02 -2.511348E-03
  12 -6.141829E-03  8.876670E-03  9.186548E-03  6.449519E-03 -6.634393E-03
  13  1.131178E-03 -4.200063E-04 -1.016255E-05 -1.510764E-02  2.598603E-02
  14  1.070207E-03 -4.879721E-03 -1.405763E-03  2.782561E-02  1.109159E-02
  15 -1.655723E-03  2.936403E-03  1.590250E-03 -3.800617E-03 -5.299978E-03
  16 -5.901058E-04  2.125121E-03  8.436201E-04 -4.377328E-03 -1.041980E-02
  17 -3.846097E-05  1.373446E-04 -5.110873E-05 -1.966200E-03 -1.326630E-03
  18  1.237235E-04 -6.688404E-04 -3.383283E-04  1.998806E-03  9.666394E-04
  19 -1.173074E-01 -1.094637E-01  3.812270E-02 -1.150648E-02 -3.048214E-02
  20 -1.130304E-01 -2.317935E-01  6.339941E-02  1.986910E-03 -2.210707E-03
  21  4.106264E-02  6.657354E-02 -6.890803E-02 -4.891653E-03 -1.331228E-02
  22 -1.084907E-01  1.054392E-01  4.532612E-02 -1.429915E-02  2.798514E-02
  23  1.080574E-01 -2.318369E-01 -7.814281E-02  1.958646E-04 -1.413140E-03
  24  4.718613E-02 -7.944934E-02 -7.820947E-02 -6.806352E-03  1.139206E-02
  25 -5.024001E-02 -1.452310E-03  1.352202E-02  2.649424E-03  5.370487E-05
  26 -1.826418E-03 -4.918181E-02  1.368002E-02  3.639358E-04 -2.231746E-03
  27  1.452739E-02  1.321935E-02 -3.075969E-01  3.084118E-03  4.864820E-04
  28 -2.538287E-04  1.656919E-03 -3.835681E-04  1.146800E-02 -5.379098E-04
  29 -2.614891E-04  1.640485E-03  1.317667E-03 -2.194747E-02 -5.552470E-03
  30 -5.123418E-04 -7.816618E-04  9.256446E-04  4.276077E-03  2.772825E-03
  31  1.135445E-04 -1.452176E-04 -8.656111E-05  2.617790E-04 -3.392604E-03
  32 -1.812774E-05  4.009060E-05 -2.733422E-05 -2.768754E-06  1.079156E-03
  33  1.734414E-04 -2.531512E-04 -1.627890E-04  2.129085E-04  2.837961E-03
  34  1.355931E-04  5.585949E-04  1.242287E-04 -3.382290E-03 -6.716188E-03
  35 -4.872590E-04 -5.381049E-04  8.740019E-05  2.386577E-03  1.169051E-03
  36 -5.601811E-05  5.784216E-05  3.629654E-05 -4.393252E-04 -2.036535E-03
  37  2.436439E-03  9.573235E-04 -1.428457E-02 -4.082285E-02  5.078931E-03
  38 -1.454727E-03  2.951483E-03  6.410734E-03  5.713458E-03 -4.965616E-02
  39  1.897772E-04  1.530101E-03 -2.357119E-02 -1.434384E-02 -2.050847E-02
  40 -1.955888E-03  2.486889E-03  3.253569E-03  1.837701E-02 -2.956220E-03
  41  2.542492E-03 -1.906310E-03 -3.832832E-03 -4.464500E-03 -1.733952E-02
  42  2.717630E-03 -3.728952E-03 -5.891615E-03 -3.269098E-02  4.798331E-02
  43  8.508411E-05 -7.230364E-04 -2.827313E-04  2.127656E-03  3.123252E-03
  44 -6.330762E-04 -4.139792E-05  2.982404E-03  9.251580E-03  9.058447E-03
  45  1.022238E-03  7.803387E-04 -3.140184E-03 -1.500650E-02 -1.504003E-02
   6
   6  1.891258E-01
   7 -1.215664E-02  3.788865E-01
   8 -5.477972E-03  3.522318E-01  5.287214E-01
   9 -7.781747E-02 -9.765378E-03 -1.866249E-02  5.855060E-02
  10 -9.889992E-03  2.396759E-02 -1.220042E-02 -2.326645E-03  5.719330E-01
  11  2.818519E-02 -1.309695E-02 -6.810470E-02 -4.378007E-03  1.426693E-01
  12 -7.674009E-02 -5.391740E-03 -4.888372E-03  1.843096E-02  2.138924E-02
  13  4.070270E-03 -7.033202E-03 -8.498340E-03 -5.190194E-05 -1.995417E-01
  14 -2.840603E-03 -4.900019E-04 -1.944517E-03  1.739582E-04 -1.953501E-03
  15 -3.667065E-03  7.420796E-04  8.735631E-04  6.980367E-04  4.548669E-02
  16 -1.372223E-03  3.643146E-03  1.342802E-03 -5.934102E-04 -2.550442E-02
  17  5.098645E-04  2.126253E-03  8.719094E-04 -4.502895E-04 -1.889224E-03
  18  8.865701E-04 -8.116343E-05 -7.626028E-05  1.420408E-05  5.665637E-03
  19  1.334386E-02 -6.906796E-03  8.975771E-04 -4.252507E-03  4.914523E-04
  20 -1.590831E-04 -6.971463E-05  2.612244E-03  2.964627E-04  6.419663E-04
  21  2.834154E-03 -4.398264E-03  2.520566E-04  6.041701E-05  4.262514E-04
  22  1.165565E-02  3.241029E-03 -2.258676E-03 -1.202332E-03 -5.242114E-03
  23  1.894415E-04 -8.590803E-04  6.960479E-04  5.511079E-05  3.822324E-04
  24  3.123534E-03  1.491534E-03  2.781627E-04 -2.725460E-04 -3.734763E-03
  25 -3.100032E-02  3.254835E-04  1.023198E-03  3.133684E-03  1.965670E-04
  26  4.697291E-04 -6.581400E-04 -1.149472E-05  3.887231E-04  1.011431E-05
  27 -1.364797E-02 -4.418780E-04 -4.524588E-05  2.314014E-03 -9.033280E-04
  28  5.710707E-03 -1.280890E-04  4.775850E-03 -7.659709E-04 -1.680027E-01
  29 -1.139323E-02  2.806879E-03 -7.685155E-03  1.095925E-03 -1.329562E-01
  30 -6.854407E-04 -1.024416E-04  3.779371E-03  1.886351E-04 -1.162827E-01
  31  2.005472E-03  1.167707E-03  1.322100E-03 -4.103378E-04 -1.358718E-02
  32 -9.255338E-04 -2.058354E-04 -3.552785E-04  1.073493E-03 -6.075124E-04
  33 -8.086579E-04 -8.561612E-04 -1.341512E-03  9.668297E-04  6.813461E-03
  34 -3.866991E-04  3.057775E-03  2.934189E-03  5.583282E-04 -2.477499E-02
  35 -1.363596E-03  1.423101E-03 -3.203031E-03 -1.841376E-04 -2.856143E-03
  36  1.493745E-03  1.712722E-03  1.266629E-04 -1.558178E-03  4.547418E-03
  37 -1.066942E-02  2.756671E-03 -1.106440E-02  1.586406E-02  5.746055E-03
  38 -5.113982E-02 -1.461452E-02 -6.799558E-03  3.087400E-02  2.723057E-02
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  36
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  42 -3.825672E-05 -2.785311E-02  4.176285E-02 -1.626648E-02  4.401337E-02
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  45 -8.076661E-05 -1.412104E-01 -1.576788E-01 -1.548879E-01 -2.413239E-03
  41
  41  6.428960E-02
  42 -6.887696E-02  8.438787E-02
  43  3.043791E-03 -1.150293E-03  1.677703E-01
  44 -3.318060E-03 -2.087719E-05  1.773877E-01  2.214424E-01
  45 -8.924798E-04 -4.119387E-03  1.499941E-01  1.709621E-01  1.681916E-01
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_ts_irc_0002 opt_ts-irc-0002.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_ts-irc-0002.in
Output files