Orca
Orca is a free software for all types of QM calculations.
Documentation and tutorials are here: https://www.orcasoftware.de/tutorials_orca
The current version is 5.0.3.
It is installed on Aurora:
module add GCC/11.2.0 OpenMPI/4.1.1 ORCA/5.0.3-static
Then, it is run by
orca input_file >output
Avogadro is a good option to illustrate Orca output
This is a simple sample input file:
! RHF def2-SVP # Level of theory.
!
SP
# Single-point energy calculation; it is default or
!
OPT
# Geometry optimisation
* xyz 0
1
# Charge, and multiplicity followed by coordinates in Å (can be changed to a.u. by %coords Units bohrs)
h
1.57623125918282
-1.40098816005358 1.92944524289998
c
3.11804788185000
-1.26044723466300 3.33347664459600
h
4.63927730299500
-2.45475405971100 2.62293967273200
h
3.85126156558200
0.66329382213900 3.40150678020000
h
2.59270405690800
-1.91429242685700 5.21564372964000
*
Alternatively, internal coordinates can be used:
* int 0 2
O 0 0 0 0.0 0.0 0.0
H 1 0 0 0.9903 0.0 0.0
*
Alternatively, an xyz file can be used:
* xyzfile 0 2 hydroxide.xyz
File:
2 # number of atoms; next line blank or title
0
O 0 0 0
H 0 0 0.9903
Alternatively, an pdb file can be used:
* pdbfile 0 2 hydroxide.pdb
Input file is not case sensitive.
Constraints:
%geom
Constraints
{B 0 1 1.25 C} # Bond length constraint
end
end
Cartesian coordinate constraints:
%geom
Constraints
{ C 3 C } # Atom 4 is fixed
{C 10:17 C} # A list of atoms is also allowed
end
end
Note that Orca number atoms starting with 0, which may be very confusing in the beginning.
Options
Use RI and RIJCOSX (exchange)
!B3LYP def2-SVP def2/J RIJDX RIJCOSX
In fact, this is default for DFT; to turn it off, use !NORI and !NOCOSX
Dispersion correction
!D3 or !D4
Increase amount printed out (e.g. to print orbitals)
!HF def2-SVP Largeprint
Frequency calculation
!FREQ
!TightOpt or !VeryTightOpt may remove imaginary freqs
Implicit solvent (COSMO is no longer any option)
!CPCM(solvent)
or
%CPCM
EPSILON 80
REFRAC 1.33
END
or
%CPCM SMD TRUE
SMDSolven "solvent"
END
Relativistic corrections
!B3LYP ZORA ZORA-def2-TVP RIJDX SARC/J
DLPNO CC
!DLPNO-CCSD(T) def2-TZVPP def2-TZVPP/C
Change maximum number of geometry steps
%geom
maxiter 1
end
Cartesian optimisation
! COpt
SCF options
%scf
MaxIter 300
CNVDIIS 1
CNVSOSCF 1
end
Level shift
%scf
CNVShift true # default = true
LShift 0.1 # default = 0.25
ShiftErr 0.1 #default = 0.0
# more convenient:
Shift Shift 0.1 ErrOff 0.1 end
end
Output options
%output
print[p_mos] true
print[p_basis] 5
end
Paralell calculations
%pal
nprocs
20
#Maximum number of cores of your machine.
end
Point charges with file reference
%pointcharges "pointcharges.pc"
File pointcharges.pc
418 # number of point charges
0.294300
6.494988 -4.096926
-5.179739 # charge and coordinates
0.164200
7.320798 -3.807798
-6.874823
0.164200
6.417509 -5.943188
-4.694079
...
No special ending
Atomic units
Geometry options
%geom
MaxIter 200
TS_search EF
# ! OptTs
TolE 5e-6
TolRMSG 1e-4
TolMaxG 3e-4
TolRMSD 2e-3
TolMaxD 4e-3
inhess GFNFF
end
%MaxCore 2000
QM/MM with Orca
Described in the Orca manual under
8.13 ORCA Multiscale Implementation
You need a prmtop file and a pdb file (and preferably a syst1 file)
1. Make an Orca input file:
!QMMM PBE0 6-31G* D3ZERO
%qmmm
ORCAFFFilename "prmtop3.ORCAFF.prms"
QMAtoms { 0:33
642:653
2238:2239
2248:2275
4716:4718 } end
ActiveAtoms { 0:33
642:653
2238:2239
2248:2275
4716:4718 } end
end
*pdbfile 0 1 pdb3.pdb
Made from the syst1 file, but renumbering to start on 0, changing "-" to ":" and removing link atoms.
2. Convert prmtop file to Orca format
orca_mm -convff -AMBER prmtop
Gives you the file prmtop3.ORCAFF.prms
3. Finally start Orca with
orca orca.in >orca.out
This does additive QM/MM and electrostatic embedding.
You may change the charges around the junction atoms (p. 375). Orca
implements the Charge Shift (CS; default), Redistributed charge and
dipole (RCD), as well as the Z0, Z1, Z2 and Z3 methods.
%qmmm
chargeAlgeration RCD
end
4. Output:
FINAL SINGLE POINT ENERGY (MM) -32.522715848742
FINAL SINGLE POINT ENERGY -2474.898029955347
FINAL SINGLE POINT ENERGY (QM/MM) -2507.420745804089
Useful greps
# Greps for all occurrences of convergence parameters in ORCA as they're displayed after each geom opt step
grep -A8 "Geometry convergence"
grep " MAX gradient"
grep "ENERGY (QM/MM)" $1 | tail -n 1 ;
neb_energies() {
# Gets the energies of the last step
of an ORCA .NEB.log file and creates a temporary path vs energy
file.
# $1: file to grep for QM/MM energies
tail -n 30 $1 | grep energy | tail -n 1 | sed
's/energy : //g'| tr -s ' ' '\n' >
energies ;
tail -n 30 $1 | grep distance $1 | tail -n 1 | sed
"s/distance : //g" | tr -s ' '
'\n' > abscissa ;
paste abscissa energies > tmp_path_energies ;
rm -fr abscissa energies ;
}