Computational Chemistry

Convenient Softwares for Computational Chemistry

  • Chime plugin for Firefox (up to v5.0)(molecular visualization)
    • An executable can be found on polyester for this.

Gaussian Example Files

Submit File

### For multi: %NProcShared=7 in input file.
### nodes=1:ppn=8 in this file.
### Short Gaussian jobs. One node one processor core.
### Number of nodes=1: Proc core Per Node=1
#PBS -l nodes=1:ppn=8
### Output files. If not specified PBS uses the job name and ID.
#PBS -o PATH_OF_INPUT/pbs.out
#PBS -e PATH_OF_INPUT/pbs.err
### Mail to user
#PBS -m eb
### Queue name

#PBS -q default
### Job name
#PBS -N JobName
### Declare job-non-rerunable
#PBS -r n

time g09 PATH_TO_INPUT/input.com

Submit Files in a Queue

In putty when submitting a job, instead of using

qsub submit.sh

Use

qsub depend=afterany:123456 submit.sh

will make the program calculate the new job after a previous job is finished. (The previous job ID is 123456 in this case.)

Single Point

%nprocshared=7
%chk=PATH_TO_INPUT/freq.chk
#P B3P86/6-31G* sp Pseudo=Read

CO2 opt with freq

0 1
O 0.0 0.0 1.5
C 0.0 0.0 0.0
O 0.0 0.0 -1.5

Geometry Optimization

%nprocshared=7
%chk=PATH_TO_FILE/freq.chk
#P B3P86/Gen opt=(MaxCycles=200,tight,calcfc) Int=UltraFine Freq=NoRaman Pseudo=Read

CO2 opt with freq

0 1
O 0.0 0.0 1.5
C 0.0 0.0 0.0
O 0.0 0.0 -1.5

H C N O P S 0
6-31G*
****
Pd 0
lanl2dz
****

Pd 0
lanl2dz

Transition State Searching

opt=ts

%nprocshared=7
%chk=/home/bjpetro/nozaki/modredund/ts_105/freq.chk
#P B3P86/Gen opt=(ts,noeigen,MaxCycles=200,tight,calcfc) Int=UltraFine Freq=NoRaman Pseudo=Read

title

mult charge
coordinates
.
.
.

atoms 0
basis
****

atoms 0
ECP

QST3

%nprocshared=7
%chk=/home/bjpetro/nozaki/qst2/freq.chk
#P B3P86/Gen opt=(MaxCycles=300,qst3,calcfc,noeigen,tight) Freq=NoRaman Pseudo=Read int=ultrafine

start

0 1
Pd -1.46980 0.42660 -0.62520
P 0.67910 -0.67740 1.62860
C 2.25270 -0.98190 0.66970
C 2.53260 -0.33090 -0.55280
S 1.42550 0.89970 -1.28450
O 0.79690 1.60890 -0.06910
O 0.34630 0.13910 -1.98600
O 2.25240 1.80020 -2.09190
C 0.63150 -2.25140 2.62680
C 1.57230 0.14760 3.04790
C 3.71300 -0.57670 -1.25730
C 4.66050 -1.46650 -0.75410
C 4.41740 -2.10940 0.45720
C 3.23020 -1.86880 1.15120
C -2.85620 -0.65550 -1.64370
H 3.87020 -0.06550 -2.20060
H 5.57780 -1.65270 -1.30540
H 5.14520 -2.80610 0.86520
H 3.06900 -2.39390 2.08610
H -2.35230 -1.20710 -2.44580
H 2.26670 -0.50540 3.58870
H 2.11290 1.03260 2.69710
H 0.80990 0.48440 3.76020
H 1.62460 -2.54720 2.98300
H -0.02610 -2.10520 3.49200
H 0.21330 -3.04040 1.99910
C -3.62830 -1.57750 -0.71130
H -2.95440 -2.32860 -0.27830
H -4.03660 -0.99370 0.12080
H -3.49690 0.12350 -2.07310
C -4.77830 -2.29330 -1.44600
H -5.32680 -2.95300 -0.76280
H -5.49140 -1.57030 -1.85920
H -4.40360 -2.90560 -2.27560
C -2.92240 0.12930 1.98320
C -3.17910 2.24110 1.06470
C -3.77140 0.44210 3.04030
H -2.46260 -0.84770 1.88580
C -4.04240 2.62560 2.08670
H -2.91420 2.91940 0.26220
C -4.34500 1.71220 3.09550
H -3.97390 -0.30310 3.80250
H -4.46600 3.62430 2.08120
H -5.01370 1.98380 3.90690
N -2.62790 1.01220 1.00790

finish

0 1
Pd -1.04750 0.61130 -0.21870
P 1.08150 -1.82110 0.48920
C 2.71150 -0.91030 0.44100
C 2.91840 0.22950 -0.36820
S 1.61540 0.95290 -1.39510
O 0.73380 1.72500 -0.39400
O 0.81380 -0.18820 -1.93380
O 2.26840 1.83730 -2.36360
C 1.34160 -3.08950 -0.85240
C 1.28740 -2.91970 1.98690
C 4.14670 0.89320 -0.39420
C 5.20230 0.45120 0.40160
C 5.02040 -0.66000 1.22120
C 3.79380 -1.32670 1.23400
C -2.76480 -0.46240 -0.04970
H 4.25910 1.75140 -1.04750
H 6.15520 0.97240 0.37880
H 5.83210 -1.01850 1.84890
H 3.69000 -2.19410 1.87630
H -2.64090 -1.41100 -0.58490
H 2.13180 -3.61590 1.92720
H 1.38550 -2.31520 2.89440
H 0.37180 -3.51540 2.08170
H 2.27990 -3.64120 -0.72580
H 0.50750 -3.80090 -0.83700
H 1.34300 -2.57290 -1.81400
C -3.14120 -0.67250 1.40970
H -2.38100 -1.28530 1.91210
H -3.16430 0.29550 1.92190
H -3.49200 0.16870 -0.57390
C -4.51500 -1.35660 1.54820
H -4.77430 -1.50080 2.60400
H -5.30440 -0.75050 1.08840
H -4.52290 -2.34070 1.06300
C -1.70210 1.62220 2.52930
C -2.24830 3.14810 0.87330
C -2.22560 2.44830 3.51910
H -1.26900 0.65510 2.75850
C -2.79690 4.02490 1.80490
H -2.23320 3.38270 -0.18450
C -2.78560 3.67230 3.15360
H -2.19090 2.12960 4.55570
H -3.22460 4.96340 1.46840
H -3.20440 4.33650 3.90380
N -1.71120 1.96280 1.22500

transition state

0 1
Pd -1.35940 0.44500 -0.21290
P 0.46800 -1.22110 1.34090
C 2.16240 -1.20660 0.55520
C 2.42830 -0.53480 -0.65920
S 1.17360 0.42150 -1.54610
O 0.73360 1.49530 -0.53180
O 0.01850 -0.49950 -1.77560
O 1.82300 0.99870 -2.72580
C 0.34190 -3.03820 1.73890
C 1.14100 -0.93290 3.06040
C 3.70130 -0.54070 -1.23320
C 4.75430 -1.20180 -0.60310
C 4.52370 -1.85810 0.60340
C 3.24620 -1.85900 1.16650
C -2.99140 -0.75100 -0.40390
H 3.84750 -0.02600 -2.17640
H 5.74300 -1.20160 -1.05320
H 5.33300 -2.37840 1.10920
H 3.09990 -2.38820 2.10150
H -2.73330 -1.59820 -1.04980
H 1.77980 -1.73880 3.43930
H 1.69360 0.01130 3.10180
H 0.28160 -0.84490 3.73550
H 1.28920 -3.44970 2.10510
H -0.42740 -3.18250 2.50680
H 0.03520 -3.56480 0.83330
C -3.50510 -1.20230 0.95560
H -2.75630 -1.83310 1.45270
H -3.66250 -0.32600 1.59370
H -3.70670 -0.09680 -0.91590
C -4.82540 -1.98720 0.83090
H -5.18480 -2.30510 1.81710
H -5.60720 -1.37130 0.37120
H -4.70030 -2.88540 0.21340
C -2.06540 1.22830 2.59600
C -2.51290 2.91350 1.06990
C -2.59270 1.98010 3.64140
H -1.67000 0.23050 2.74890
C -3.06190 3.72180 2.06130
H -2.45820 3.24090 0.03840
C -3.10270 3.25010 3.37250
H -2.59960 1.56920 4.64560
H -3.44950 4.70050 1.79920
H -3.52320 3.85850 4.16770
N -2.02410 1.68400 1.32790

H C N O P S 0
6-31G*
****
Pd 0
lanl2dz
****

Pd 0
lanl2dz

Modredundant

%nprocshared=7
%chk=/home/bjpetro/nozaki/modredund/freq.chk
#P B3P86/Gen opt=(modredundant,MaxCycles=300,tight,calcfc) Int=UltraFine Pseudo=Read nosymm

cis/trans isom from start to end

0 1
N
Pd 1 r2
C 2 r3 1 a3
P 2 r4 1 a4 3 d4
C 3 r5 2 a5 1 d5
S 3 r6 2 a6 1 d6
O 6 r7 3 a7 2 d7
O 6 r8 3 a8 2 d8
O 6 r9 3 a9 2 d9
C 4 r10 2 a10 1 d10
C 4 r11 2 a11 1 d11
C 3 r12 2 a12 1 d12
C 12 r13 3 a13 2 d13
C 13 r14 12 a14 3 d14
C 14 r15 13 a15 12 d15
C 2 r16 1 a16 3 d16
H 12 r17 3 a17 2 d17
H 13 r18 12 a18 3 d18
H 14 r19 13 a19 12 d19
H 15 r20 14 a20 13 d20
H 16 r21 2 a21 1 d21
H 11 r22 4 a22 2 d22
H 11 r23 4 a23 2 d23
H 11 r24 4 a24 2 d24
H 10 r25 4 a25 2 d25
H 10 r26 4 a26 2 d26
H 10 r27 4 a27 2 d27
C 16 r28 2 a28 1 d28
H 28 r29 16 a29 2 d29
H 28 r30 16 a30 2 d30
H 16 r31 2 a31 1 d31
C 28 r32 16 a32 2 d32
H 32 r33 28 a33 16 d33
H 32 r34 28 a34 16 d34
H 32 r35 28 a35 16 d35
C 1 r36 2 a36 3 d36
C 1 r37 2 a37 3 d37
C 36 r38 1 a38 2 d38
H 36 r39 1 a39 2 d39
C 37 r40 1 a40 2 d40
H 37 r41 1 a41 2 d41
C 38 r42 36 a42 1 d42
H 38 r43 36 a43 1 d43
H 40 r44 37 a44 1 d44
H 42 r45 38 a45 36 d45
Variables:
r2= 2.0606
r3= 3.7539
a3= 145.05
r4= 2.4586
a4= 96.43
d4= 3.25
r5= 1.4066
a5= 71.55
d5= 345.47
r6= 1.7998
a6= 54.80
d6= 141.04
r7= 1.5345
a7= 103.29
d7= 37.05
r8= 1.4744
a8= 105.38
d8= 279.93
r9= 1.4608
a9= 106.75
d9= 153.56
r10= 1.8392
a10= 118.75
d10= 76.44
r11= 1.8424
a11= 115.15
d11= 315.24
r12= 1.3907
a12= 155.72
d12= 220.02
r13= 1.3922
a13= 120.08
d13= 115.34
r14= 1.3907
a14= 119.79
d14= 359.88
r15= 1.3933
a15= 120.01
d15= 0.18
r16= 2.0498
a16= 88.52
d16= 185.14
r17= 1.0850
a17= 118.24
d17= 295.49
r18= 1.0862
a18= 119.90
d18= 180.03
r19= 1.0864
a19= 120.33
d19= 180.09
r20= 1.0857
a20= 118.80
d20= 180.10
r21= 1.0973
a21= 109.93
d21= 345.55
r22= 1.0948
a22= 113.41
d22= 175.41
r23= 1.0938
a23= 110.03
d23= 298.16
r24= 1.0948
a24= 107.81
d24= 55.75
r25= 1.0948
a25= 111.52
d25= 177.32
r26= 1.0953
a26= 109.39
d26= 298.04
r27= 1.0921
a27= 107.42
d27= 56.57
r28= 1.5168
a28= 110.58
d28= 109.80
r29= 1.1008
a29= 110.49
d29= 296.56
r30= 1.0958
a30= 109.17
d30= 53.62
r31= 1.0952
a31= 102.91
d31= 229.05
r32= 1.5323
a32= 112.27
d32= 175.02
r33= 1.0965
a33= 111.33
d33= 180.09
r34= 1.0956
a34= 110.68
d34= 300.02
r35= 1.0968
a35= 111.30
d35= 59.66
r36= 1.3430
a36= 121.36
d36= 102.64
r37= 1.3442
a37= 120.01
d37= 281.82
r38= 1.3889
a38= 122.37
d38= 180.03
r39= 1.0841
a39= 115.91
d39= 0.57
r40= 1.3882
a40= 122.35
d40= 180.19
r41= 1.0844
a41= 115.90
d41= 359.90
r42= 1.3910
a42= 119.05
d42= 359.44
r43= 1.0848
a43= 119.50
d43= 179.81
r44= 1.0847
a44= 119.50
d44= 179.71
r45= 1.0857
a45= 120.73
d45= 180.31

1 2 3 4 3.25 S 7 25.25 <--[atom1] [atom2] [atom3] [atom4] [3.25=start val] [S=scan] [# of steps] [step size]

atoms 0
basis
****
atom 0
ecp

Specifying Basis Sets and Effective Core Potentials (ECPs) Manually

%nprocshared=7
%chk=PATH_TO_FILE/freq.chk
#P B3P86/Gen sp Pseudo=Read geom=allcheck POP=(NBO,hirshfeld,FULL) GFOLDPRINT

H C N O 0
6-31++G(d',p')
****
P 0
S 2 1.00
1.5160000 -0.5862089
0.3369000 1.2994376
S 1 1.00
0.1211000 1.0000000
P 2 1.00
3.7050000 -0.0691472
0.3934000 1.0161988
P 1 1.00
0.1190000 1.0000000
P 1 1.00
0.0298000 1.0000000
D 1 1.00
0.3640000 1.0000000
****
S 0
S 2 1.00
1.8500000 -0.5324335
0.4035000 1.2763801
S 1 1.00
0.1438000 1.0000000
P 2 1.00
4.9450000 -0.0608116
0.4870000 1.0132686
P 1 1.00
0.1379000 1.0000000
P 1 1.00
0.0347000 1.0000000
D 1 1.00
0.4960000 1.0000000
****
Pd 0
S 3 1.00
2.7870000 -1.6102393
1.9650000 1.8489842
0.6243000 0.6037492
S 4 1.00
2.7870000 1.3540775
1.9650000 -1.6780848
0.6243000 -0.8559381
0.1496000 1.0200299
S 1 1.00
0.0436000 1.0000000
P 3 1.00
5.9990000 -0.1034910
1.4430000 0.7456952
0.5264000 0.3656494
P 2 1.00
0.7368000 0.0763285
0.0899000 0.9740065
P 1 1.00
0.0262000 1.0000000
D 3 1.00
6.0910000 0.0376146
1.7190000 0.5200479
0.6056000 0.5706071
D 1 1.00
0.1883000 1.0000000
F 1 1.00
1.4720000 1.0000000
****

P 0
P-ECP 2 10
d potential
5
1 462.1211423 -10.0000000
2 93.6863701 -79.4864658
2 21.2349094 -28.3668251
2 6.3388415 -9.8577589
2 2.0620684 -1.0163783
s-d potential
5
0 78.0831823 3.0000000
1 58.9576810 12.9104154
2 36.0571255 150.0250298
2 11.2464453 71.7083146
2 2.6757561 23.0397012
p-d potential
6
0 75.1617880 5.0000000
1 57.4544041 6.3446507
2 47.9481748 198.5585104
2 18.4588360 111.1470820
2 5.9414190 40.3944144
2 1.8487507 6.4483233
S 0
S-ECP 2 10
d potential
5
1 532.6685222 -10.0000000
2 108.1342248 -85.3593846
2 24.5697664 -30.4513290
2 7.3702438 -10.3745886
2 2.3712569 -0.9899295
s-d potential
5
0 106.3176781 3.0000000
1 100.8245833 10.6284036
2 53.5858472 223.6360469
2 15.3706332 93.6460845
2 3.1778402 28.7609065
p-d potential
6
0 101.9709185 5.0000000
1 93.2808973 6.0969842
2 65.1431772 285.4425500
2 24.6347440 147.1448413
2 7.8120535 53.6569778
2 2.3112730 8.9249559
PD 0
PD-ECP 3 28
f potential
5
0 598.3336444 -0.0563177
1 162.4298290 -20.1288036
2 51.5714771 -105.8197923
2 16.4888260 -42.5733345
2 5.8287656 -3.6165086
s-f potential
5
0 73.3806304 3.0003651
1 14.7550438 32.4350093
2 17.8350204 459.0830383
2 12.7111477 -868.0629029
2 9.3292063 514.4726098
p-f potential
5
0 55.6689877 4.9593099
1 64.2337771 21.1711029
2 17.6254952 605.0560092
2 11.9058155 -726.9641846
2 8.5100832 396.3274883
d-f potential
5
0 49.9994728 3.0508745
1 39.7477547 22.2506580
2 11.4321366 674.8357698
2 9.1790080 -1040.8554048
2 7.5624429 505.9375147 

Additional Options

  • geom=allcheck

    Use this to restart your calculation from a geometry in the checkpoint file. Omit the title, multiplicity, charge and coordinates from your input file, such as in the following:

    %nprocshared=7
    %chk=PATH_TO_FILE/freq.chk
    #P B3P86/6-31G* sp Pseudo=Read geom=allcheck
  • POP=(NBO,hirshfeld,FULL)

    Add this, or a variant, to perform an NBO analysis, hirshfeld charge analysis and a full population analysis (pop=full is needed to plot orbitals in Molekel).

  • GFOLDPRINT

    Add this keyword to include a more verbose output in the computational logfile. Specifically, this causes the printing of the molecules grid data which is necessary for plotting orbitals in Molekel.

  • GFPRINT

    This keyword can be used to see how the atoms of your computation are handled with the basis set you have selected. This means you can see the distribution of functions per atom which you have selected. This is a good way to learn the differences between STO, double-zeta, and triple-zeta quality basis sets.