Molecular Builders and Single
Point Calculation
Esmaeil Farajpour Bonab, October 8, 2019
Molecular Structure Specification
● Cartesian coordinates:
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Molecule with N atoms 3N Cartesian coordinates
O -0.455432366 0.000000000 -1.763659097
H -0.455432366 0.759337000 -1.167616097
H -0.455432366 -0.759337000 -1.167616097
Element X(Å) Y(Å) Z(Å)
● Internal Coordinate: a systematic approach to build Z-matrix (a list of internal coordinates)
● nonlinear molecule: 3N-6 H2
O =3 internal coordinates (two bonds (A) and one angle (B))
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No. Element A Bond
length (Å)
B Bond Angle (degrees)
1 O
2 H 1 0.959
3 H 1 0.959 2 103.9
1 H
2 O 1 0.959
3 H 2 0.959 1 103.9
1
2 3
1
2
3
● For molecules if N => 4, there is an additional parameters called dihedral (torsion) angle.
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b
1
b
2
b
3
b
3
b
1
𝛷
𝛷
No. Element A Bond
length
(Å)
B Bond angle
(degrees)
D Dihedral angle
(degrees)
1 C
2 H 1 1.089
3 H 1 1.089 2 109.471
4 H 1 1.089 2 109.471 3 120.000
5 H 1 1.089 2 109.471 3 -120.000
Builders in Wolf Computers
Gabedit04
● Free
● Relatively slow
● https://sites.google.com/site/allouc
hear/Home/gabedit
Nemesis03
● Developed by Petr Kulhanek
● https://nemesis.ncbr.muni.cz
Gaussview02
● Comercial
● Ability of generating specified parameters
● https://gaussian.com/gv6main/
Avogadro01
● Cross-platform (windows, Linux, Mac OS X)
● Free, Open Source
● Fast
● https://avogadro.cc
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Task (I)
Open Avogadro and Gaussview using the following commands:
Open a terminal (Ctrl+Alt+T)
$module add avogadro
$avogadro
● H2
O
● CH2
CHCHCH2
● Benzylamine (C6
H5
CH2
NH2
)
$module add gaussview
$gv
● NH2
CH3
● CH3
CH2
OH
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Typical Gaussian input file for SP
%chk=<name>.chk
%mem=<int>gb
%nproc=<int>
# b3lyp/6-31g
Title Card Required
0 1
6 0.753169000 3.160531000 -2.318531000
6 1.979701000 2.378550000 -2.303684000
6 0.382563000 3.894249000 -1.178245000
6 2.803075000 2.378437000 -1.170502000
6 3.406284000 1.133090000 -0.722816000
6 3.269679000 -0.083775000 -1.462575000
6 3.422882000 -1.301939000 -0.725708000
6 -1.973088000 3.160186000 -1.432584000
….
wavefunction
Number of shared
processor and the value
of memory usage
Command line: opt or sp,
function, basis set, other
relevant commands
Charge and
multiplicity (2S+1)
Cartesian coordination
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Single Point (SP) Calculation
Workflow for Gaussian (https://gaussian.com)
● Create input file using any builders (for example: Gaussview or Avogadro)
● Specify the method (Function and basis set)
● For single point use SP in command line.
● Save the .chk file
● Specify the number of cpus and the memory value
● Save the input file as “.com” or “.gjf”
● if you don’t specify the version of the software, automatically the latest version of the code will be
added up.
● Prepare the file (for example run.sh) for job submission including the following commands:
#!/usr/bin/env infinity-env
module add gaussian:16.A3
g16 <inputfile>.gjf
● Submit the prepared job as follows:
$psubmit default run.sh ncpus=<int>,mem=<int>gb,walltime=<int>:<int>:<int> -y
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Logfile and .chk file
One can extract the energy, structure,and other relevant results using logfile.
.chk file is a binary file. In order to convert it into a human readable file, one can
use the following command:
$ formchk -3 <name>.chk
The created <name>.fchk file can be used for analyzing of orbital, electron
density.
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● Prepare the input file using any builder
● Add turbomole module: $module add turbomole
● Convert the prepared input file to the turbomole input file using the command: x2t
<filename>.com > coord
● execute define (as the interface between user and code) command: $define
● Two first items can be skipped.
● Molecular geometry specification:
● Add atomic coordinate using a <file> command
● Create internal coordinate using ired coomand
● Terminate using * and go through the next step.
● Basis set specification:
● Using b one can assign the basis set for all atoms like b all def-SVP or using b “atom
nickname” def-SVP. For example: b “cl” def-SVP
● bl can list the type of specified basis sets for each atom
● Use * to terminate this section and keep continue.
SP calculation using Turbomole
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● Initial guess using extended Huckel theory (eht) and carefully specified the item which you are
being asked.
● Method specification:
● Execute dft and specified the status of DFT options as follows:
● Execute on in order to activate DFT method.
● Specify function using func command.
● Change the grid size using grid command.
● Terminate this section using * and go through the next step.
● RI parameters:
● On command activates this option
● m can change the usage memory for this item using for example m 3000
● Terminate using *.
● dsp (Dispersion correction) :
● on command to switch DFT-D3
● Terminate using *.
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● After finishing all the mentioned commands, use * to complete the define section.
● One should provide coord, control, mos, basis and auxbasis files.
● submit the run_turbo.sh job including the following commands for SP calculation.
#!/usr/bin/env infinity-env
Module add turbomole
ridft > dft.out
● For normal geometry optimization, one should use jobex command as follows:
#!/usr/bin/env infinity-env
Module add turbomole
jobex -ri > dft.out
● http://www.turbomole-gmbh.com/32-newsmp/75-turbomole-version-74.html
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Output files for Turbomole
● job.start: informs you about the current option
● converged: convergence is signalled by this file otherwise you should find
not.converged file.
● job.last: last complete cycle
● mos: molecular orbitals
● dft.out: optimization procedure
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