Thise are some of Gaussian 98 tips that could be useful to start learning the software. In this stage, you are already able to use gaussian technically. This tips and manual is taken from the website of http://www.theorie.physik.uni-muenchen.de/~dahlke/computer/gaussianHowto.html
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1.How to write output file that can be visualized by MOLDEN?
Answer:
Add this line to the beginning of your input file:
#gfinput iop(6/7=3)
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2.How to gather output information from the .log file?
Answer:
a)grep “SCF Done” file.log
A sample output:
SCF Done: E(RHF) = -78.0316815007 A.U. after 5 cycles
b)grep “[MR].[xS]…. [FD]” file.log
A sample output:
Maximum Force 0.011236 0.000450 NO
RMS Force 0.006520 0.000300 NO
Maximum Displacement 0.018882 0.001800 NO
RMS Displacement 0.017479 0.001200 NO
Maximum Force 0.002858 0.000450 NO
RMS Force 0.001662 0.000300 NO
Maximum Displacement 0.004150 0.001800 NO
RMS Displacement 0.004179 0.001200 NO
Maximum Force 0.000156 0.000450 YES
RMS Force 0.000094 0.000300 YES
Maximum Displacement 0.000413 0.001800 YES
RMS Displacement 0.000311 0.001200 YES
Maximum Force 0.000156 0.000450 YES
RMS Force 0.000094 0.000300 YES
Maximum Displacement 0.000848 0.001800 YES
RMS Displacement 0.000779 0.001200 YES
(CARE:the above commands are case sensitive)
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3.How to restart a previous calculation?
Answer:
You must have a checkpoint file to do so.
The sample input file is as follows:
%chk=chkfile //chkfile is the name of the checkpoint file saved previously
#p gfinput iop(6/7=3)
#QCISD/6-31G(d) //you can also write QCISD chkbasis which reads basis settings from checkpoint file
#opt=(maxcycle=350) scf(maxcycle=300)
#geom=allcheck nosym
#guess=read //careful,guess=read option reads wavefunction from the checkpoint file
//you should do this only if the basis set is consistant
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4.How to compare the influence of different basis sets?
Answer:
Generally,we start from an optimized structure read in from an checkpoint file.
Here is a sample input file:
%chk=chkfile //chkfile is the name of the checkpoint file saved previously
#p gfinput iop(6/7=3)
#QCISD/6-31G(d)
#opt=(maxcycle=350) scf(maxcycle=300)
#geom=allcheck nosymm
–Link1–
%chk=chkfile
#p gfinput iop(6/7=3)
#QCISD/6-311G+(d) //change of basis
#opt=(maxcycle=350) scf(maxcycle=300)
#geom=allcheck nosymm
–Link2–
……
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5.How to kill a job on Leland system?
Answer:
a)jobs
kill %1
b)ps -fu bshan
kill 21983
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6.How to fix certain atoms?
Answer:
you need to use the Modredundant keyword to the route section
A sample input:
#gfinput iop(6/7=3)
#B#LYP/6-31G(d) Opt(Modredundant)
title section
0 1
Molecular specification(in Z-matrix form)
N1 B //generate Cartesian coordinates involving atom N1
…
* F //Freeze all Cartesian coordinates
in this case,atom N1 is freezed while others are free to move.
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7.How to do partial Optimization?
Answer:
after Molecular specification section, add lines like:
N1 N2 F
N1 N2 N3 N4 F
in this case,bond length between atom N1 and N2 are fixed. Similarly, the dihedral angle
formed by N1 N2 N3 and N4 is also fixed.
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8.How to use split Basis Sets for different atoms
Answer:
We may need a larger basis to describe the atoms involved in reaction, while describing
the rest of the system with smaller basis sets.
In this case, we need the “Gen” keyword
A sample input:
#gfinput iop(6/7=3)
#B3LYP/Gen Opt
……
N1 N2 N3 0
6-311++G(d,p)
****
N4 N5 N6 0
6-31G
****
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9.How to locate transition state?
Answer:
A sample route section
#gfinput iop(6/7=3)
#B3LYP/6-31G(d) Opt(TS,Noeigen)
In order to increase the efficiency of the saddle point search,we could calculate
the force constants by adding “CalcFC” keyword.
#gfinput iop(6/7=3)
#B3LYP/6-31G(d) Opt(TS,Noeigen,CalcFC)
We can also ask Gassian to automatically generate a gues structure for the reaction
by using keyword “QST3″ or “QST2″
#gfinput iop(6/7=3)
#B3LYP/6-31G9d) Opt(QST3,Noeigen,CalcFC)
A+B–>C Reactant //title section
0 1
structure of A+B
A+B–>C Product
0 1
structure of C
A+B–>C TS
0 1
guess structure for the TS
Note:the corresponding atoms need to appear in the same order within all the molecule specifications.
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10.How to characterize a Transition State?
Answer:
If a transition state search is successful,at least there should be one and only one imaginary frequency.
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11.How to carry out a compound job?
Answer:
#gfinput iop(6/7=3)
#G2 Opt(TS,Noeigen) //you can replace G2 with CBS-Q or some other methods.
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12.How to modifying Optimized Structures?
Modify it by substituting atoms or groups: For example, you could change a hydrogen to a methyl group by editing
the structure, replacing the desired hydrogen with a carbon atom, and then adding three additional hydrogen
atoms bonded to that carbon. The latter could be given in internal coordinates:
H6 1.2 2.3 1.1 H6 1.2 2.3 1.1
H7 1.2 0.0 -.9 C7 1.2 0.0 -.9
H8 0.0 -.9 0.0 H8 0.0 -.9 0.0
H9 C7 R H5 A C2 180.0
H10 C7 R H6 A C2 180.0
H11 C7 R H8 A C2 -180.0
R=1.0
A=120.0
7 2 1.5
The new structure on the right also uses an additional redundant internal coordinate (specifying Opt=ModRedundant
on the final job) to alter the bond distance for the new carbon atom which is replacing the hydrogen (bonded to atom 2).
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13.How to carry out PES?
Relaxed PES Scans. For Opt=Z-matrix, a relaxed PES scan is requested simply by tagging the Z-matrix variables whose
values are to be incremented with the S code letter and the number of steps and the increment size. For example, the
following input file requests a relaxed PES scan for the given molecule:
# HF/6-31G(d) Opt=Z-matrix Test
Relaxed PES scan
0 1
O
H 1 R1
C 1 R2 2 A2
…
Variables:
R1 0.9 S 5 0.05
R1 1.1
A2 115.4 S 2 1.0
…
This causes the variable R1 to be incremented five times, by 0.05 ? each time, and the variable A2 to be incremented
twice, by 1 degree each time, resulting in a total of 18 geometry optimizations (the initial values for each variable
also constitute a point within the scan).
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14.How to visualize orbitals?
By default, natural orbitals are not included in the checkpoint file. Use a second job step of this form to place
the natural orbitals into the checkpoint file:
–Link1–
%Chk=name
# IOP(4/5=8,4/38=-1) Guess=(Read,Save,Only) Geom=AllCheck
Run the formchk utility on the resulting checkpoint file to prepare the orbitals for visualization.
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16.Green’s function
ROVGF and UOVGF Keywords
These method keywords request an Outer Valence Green’s Function (propagator) calculation of
correlated electron affinities
and ionization potentials
Use Iop(9/11=100) to specify the starting and ending orbitals to refine as input (in
a separate input section with a terminal blank line). By default, all orbitals are used.
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17.How to use KMLYP
#BLYP/6-31G* Opt(Maxcycles=199) Freq
#iop(5/45=10000557) iop(5/46=00000443) iop(5/47=04481000)
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18.How to output the Fock Matrix and Overlap Matrix?
Fock Matrix : iop(5/33=3)
Overlap Matrix : iop(3/33=1)
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19.How to assign fictitious value in the freq calculation to decouple the modes?
Answer: in the route section,add freq(ReadIsotopes)
after molecular specification section,add another section(in section priority order)
298.0 1.0
28
28
1000.0 <–fictitious mass
1000.0
1000.0
1
1
1
Prof. Debashis Bandyopadhyay said,
June 26, 2007 at 9:08 am
I am trying to optimized a structure which is basically connection between two parallel graphite planes through two Li atoms. I do not want to change any internal coordinates of the graphite structures, but I can varry the coordinates of Li atoms keeping them in the layers of twi graphite planes. I do not know how to fixed the internal parameters of the graphie planes.
Looking forward for your help.
Thnaks,
Debashis
superbeton said,
June 26, 2007 at 10:57 pm
Dear: Prof. Debashis B.
Thank you. I will try to answer your question but if you feet that it is not clear, you can ask me again.
From your question, it looks that you want to do ‘partial’ optimization of the distance between Li and graphite only.
In Gaussian, there is a possibility to do partial optimization by some ways. The first, probably you already know it by fixing specific variable and put F (Frezze) next after you difine the variable. It is burdening for large molecule geometry, such as your case.
Another way is by separating the constants and variable in your input section. You can do it by make a blank line or a line containing a space in the first column and put the string Constants:
For example for water, I want to keep the angel of H-O-H, but i want to optimize the H-O distance:
# HF/6-31G(d) Opt Test
Partial optimization for water
0 1
O
H1 O R
H2 O R H1 A
Variables:
R 1.0
Constants:
A 105.4
I don’t know whether it works in cartesian input coordinat or not, caused usually I work on Z-matrix. And for your case, probably you can have R as the distance between Li-graphite and/or dihedral angel of Li to the graphite (depend on what you want and your geometry).
For others, you can put under the ‘constants’.
Oke, I hope this answer is what you want. Or if not, please let me know it.
Thnak you
benjamin said,
September 22, 2007 at 7:16 am
Thank you, I am novice in gaussian and it served me a lot your help
snoze said,
March 30, 2008 at 9:39 pm
Hi, I am trying to setup a Gaussian calculation. In my calculation I want to split the atoms in two layers. I want to treat inner layer with different basis set and outer layer with different basis set. Do I need to fix the outer atoms when optimizing the inner atoms and vice versa.
Thanks you very much for your time and help.
snoze said,
March 30, 2008 at 9:52 pm
Dear Sir,
How can I use different basis set for different atoms in same molecule. In doing so, do i need to fix the second set when optimizing the first and vice versa.
thanks you