Example -- I want to do explicit solvent modelling of methanol in water. This is obviously an articifical approach, but generally applicable.
This is a rough approach to doing oniom calculations using gaussian 09
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 g03.g03in:
1 %nprocshared=4
2 %Chk=g09_oniom.chk
3 #P rb3lyp/GEN 5D Opt=() Freq=() Punch=(MO) Pop=() scrf=(pcm,solvent=water)
4
5 g09_oniom
6
7 0 1 ! charge and multiplicity
8 C 0.00000 0.00000 0.00000
9 H -0.675500 -0.675500 0.675500
10 H 0.675500 -0.675500 -0.675500
11 H -0.675500 0.675500 -0.675500
12 O 0.866025 0.866025 0.866025
13 H 1.51843 0.213620 1.51843
14
15 H 0
16 S 3 1.00
17 18.73113700 0.03349500
18 2.82539400 0.23472700
19 0.64012200 0.81375700
20 S 1 1.00
21 0.16127800 1.00000000
22 ****
23 O 0
24 S 6 1.00
25 5484.67170000 0.00183100
26 825.23495000 0.01395000
27 188.04696000 0.06844500
28 52.96450000 0.23271400
29 16.89757000 0.47019300
30 5.79963500 0.35852100
31 SP 3 1.00
32 15.53961600 -0.11077800 0.07087400
33 3.59993400 -0.14802600 0.33975300
34 1.01376200 1.13076700 0.72715900
35 SP 1 1.00
36 0.27000600 1.00000000 1.00000000
37 SP 1 1.00
38 0.08450000 1.00000000 1.00000000
39 D 1 1.00
40 0.80000000 1.00000000
41 ****
42 C 0
43 S 6 1.00
44 3047.52490000 0.00183500
45 457.36951000 0.01403700
46 103.94869000 0.06884300
47 29.21015500 0.23218400
48 9.28666300 0.46794100
49 3.16392700 0.36231200
50 SP 3 1.00
51 7.86827200 -0.11933200 0.06899900
52 1.88128800 -0.16085400 0.31642400
53 0.54424900 1.14345600 0.74430800
54 SP 1 1.00
55 0.16871400 1.00000000 1.00000000
56 SP 1 1.00
57 0.04380000 1.00000000 1.00000000
58 D 1 1.00
59 0.80000000 1.00000000
60 ****
This is a rough approach to doing oniom calculations using gaussian 09
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 g03.g03in:
1 %nprocshared=4
2 %Chk=g09_oniom.chk
3 #P rb3lyp/GEN 5D Opt=() Freq=() Punch=(MO) Pop=() scrf=(pcm,solvent=water)
4
5 g09_oniom
6
7 0 1 ! charge and multiplicity
8 C 0.00000 0.00000 0.00000
9 H -0.675500 -0.675500 0.675500
10 H 0.675500 -0.675500 -0.675500
11 H -0.675500 0.675500 -0.675500
12 O 0.866025 0.866025 0.866025
13 H 1.51843 0.213620 1.51843
14
15 H 0
16 S 3 1.00
17 18.73113700 0.03349500
18 2.82539400 0.23472700
19 0.64012200 0.81375700
20 S 1 1.00
21 0.16127800 1.00000000
22 ****
23 O 0
24 S 6 1.00
25 5484.67170000 0.00183100
26 825.23495000 0.01395000
27 188.04696000 0.06844500
28 52.96450000 0.23271400
29 16.89757000 0.47019300
30 5.79963500 0.35852100
31 SP 3 1.00
32 15.53961600 -0.11077800 0.07087400
33 3.59993400 -0.14802600 0.33975300
34 1.01376200 1.13076700 0.72715900
35 SP 1 1.00
36 0.27000600 1.00000000 1.00000000
37 SP 1 1.00
38 0.08450000 1.00000000 1.00000000
39 D 1 1.00
40 0.80000000 1.00000000
41 ****
42 C 0
43 S 6 1.00
44 3047.52490000 0.00183500
45 457.36951000 0.01403700
46 103.94869000 0.06884300
47 29.21015500 0.23218400
48 9.28666300 0.46794100
49 3.16392700 0.36231200
50 SP 3 1.00
51 7.86827200 -0.11933200 0.06899900
52 1.88128800 -0.16085400 0.31642400
53 0.54424900 1.14345600 0.74430800
54 SP 1 1.00
55 0.16871400 1.00000000 1.00000000
56 SP 1 1.00
57 0.04380000 1.00000000 1.00000000
58 D 1 1.00
59 0.80000000 1.00000000
60 ****
2. Solvation using gromacs
Take the output, g03.g03out, and use babel to export the optimised structure
babel -ig09 g03.g03out -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
Because I'm lazy, I then add an extra column for high/low, chop off the first few lines, and add a column with zeros...because that works. Not sure what that's actually for. Molecule?
tail -n +3 solvated.xyz | gawk '{print $1,"0",$2,$3,$4,"Low"}'>oniom.xyz
Edit oniom.xyz by hand and change the lines with "Low" to "High" (or just H) for the atoms in the methanol molecule.
C 0 10.14000 10.34000 10.00000 High
H 0 9.65000 10.75000 10.90000 High
H 0 9.65000 10.75000 9.10000 High
H 0 11.19000 10.65000 10.00000 High
O 0 10.14000 8.91000 10.00000 High
H 0 9.22000 8.60000 10.00000 High
O 0 5.69000 12.75000 11.65000 Low
H 0 4.76000 12.68000 11.28000 Low
H 0 5.80000 13.64000 12.09000 Low
O 0 15.55000 15.11000 7.03000 Low
[..]
cp oniom.xyz oniom.in
Edit oniom.in and put in your gaussian instructions, e.g.:
%chk=methanol_explicit.chk
%mem=500MB
%nprocshared=3
#Oniom(rb3lyp/6-31+g*:uff) maxdisk=6000MB opt=()
Methanol in explicit water
0 1 0 1 0 1
C 0 10.14000 10.34000 10.00000 High
[...]
So, you specify Oniom(high level:low level) -- here dft and MM (via uff -- amber and charmm are available too -- but then you must carefully define the atom types. See here).
You don't always, but sometimes, have to specify the spin/multiplicity of the high and low level systems as well as the total spin and multiplicity. Anyway, you can: First the overall, the the high, then the low level. E.g. we have a chromium compound with an unpaired spin of 1 (multiplicity=2) and a charge of +3, and have a MM shell with five sodium atoms and a multiplicity of 1 (spin=0). The total charge is 8 and total multiplicity is 2. The line would read 8 2 3 2 0 1.
That's it! You're ready to roll.
The run takes about 3 minutes.
That's it!
You don't always, but sometimes, have to specify the spin/multiplicity of the high and low level systems as well as the total spin and multiplicity. Anyway, you can: First the overall, the the high, then the low level. E.g. we have a chromium compound with an unpaired spin of 1 (multiplicity=2) and a charge of +3, and have a MM shell with five sodium atoms and a multiplicity of 1 (spin=0). The total charge is 8 and total multiplicity is 2. The line would read 8 2 3 2 0 1.
That's it! You're ready to roll.
The run takes about 3 minutes.
That's it!
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