This is a rough approach to doing oniom calculations using nwchem 6.0 -- this is a technical description, not a how-to when it comes to the science.
1. Pre-optimisation
Draw methanol and set up a simple calc using e.g. ecce to pre-optimise the structure with e.g. an implicit solvent model. Here's nwch.nw:
scratch_dir /scratch
Title "pre-oniom"
Start pre-oniom
echo
charge 0
geometry autosym units angstrom
C 0.00000 0.00000 0.00000
H -0.675500 -0.675500 0.675500
H 0.675500 -0.675500 -0.675500
H -0.675500 0.675500 -0.675500
O 0.866025 0.866025 0.866025
H 1.51843 0.213620 1.51843
end
ecce_print /home/me/jobs/jobs/testing/old/pre-oniom/ecce.out
basis "ao basis" spherical print
H library "6-31+G*"
O library "6-31+G*"
C library "6-31+G*"
END
dft
mult 1
XC b3lyp
mulliken
end
driver
default
end
cosmo
end
task dft optimize
task dft freq
2. Solvation using gromacs
Take the output, nwch.nwout, and use babel to export the optimised structure
babel -inwo nwch.nwout -oxyz molecule.xyz
The next few steps require gromacs:
editconf -f molecule.xyz -o molecule.gro -box 2 2 2
genbox -cp molecule.gro -cs spc216.gro -o solvated.gro
babel -igro solvated.gro -oxyz solvated.xyz
tail -n +3 solvated.xyz > oniom.nw
3. Putting it all together
The only 'trick' is how to define what part of the input belongs to the high level section and what belongs to the low level section -- for a solvation case like this, where whole molecules are treated by one method or another, use model. The last atom to be part of the high level section is the last of the six atoms in methanol, so the keyword is model 6. Atoms 7 to infinity are thus part of the sto-3g part, and atoms 1-6 part of the 6-31g* part.
memory stack 600 mb heap 200 mb global 800 mb
scratch_dir /scratch
Title "oniom"
Start oniom
echo
charge 0
geometry units angstrom
symmetry c1
C 10.12000 10.35000 10.00000
H 9.60000 10.72000 10.89000
H 9.60000 10.72000 9.11000
H 11.14000 10.74000 10.00000
[.]
H 0.46000 2.39000 6.86000
H 1.16000 1.73000 8.18000
end
basis sto-3g spherical
* library sto-3g
end
basis 6-31g spherical
* library 6-31g
end
oniom
model 6
low dft basis sto-3g input "dft\; xc\; end"
high dft basis "6-31g" input "dft\; xc\; end"
end
basis "ao basis" spherical print
H library "6-31+G*"
O library "6-31+G*"
C library "6-31+G*"
END
task oniom
This takes forever to run, but run it does. The memory statement is important -- if the global memory is too small it will crash. Also, be aware that the amount of memory specified is per instance -- if you launch with mpirun -n 3, multiply by 3 to get the amount of memory that needs to be present (here, 2.4 GB physical RAM).
