# Constraint algorithmsΒΆ

Constraints are defined in the `[ constraints ]`

section. The format is two atom numbers
followed by the function type, which can be 1 or 2, and the constraint
distance. The only difference between the two types is that type 1 is
used for generating exclusions and type 2 is not (see sec. Exclusions).
The distances are constrained using the LINCS or the SHAKE algorithm,
which can be selected in the mdp file. Both types of constraints can be
perturbed in free-energy calculations by adding a second constraint
distance (see Constraint forces). Several types of bonds and
angles (see Table 14) can be converted automatically to
constraints by grompp. There are several options for this in the mdp
file.

We have also implemented the SETTLE algorithm 47, which is an analytical solution of SHAKE, specifically for water. SETTLE can be selected in the topology file. See, for instance, the SPC molecule definition:

```
[ moleculetype ]
; molname nrexcl
SOL 1
[ atoms ]
; nr at type res nr ren nm at nm cg nr charge
1 OW 1 SOL OW1 1 -0.82
2 HW 1 SOL HW2 1 0.41
3 HW 1 SOL HW3 1 0.41
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16333
[ exclusions ]
1 2 3
2 1 3
3 1 2
```

The `[ settles ]`

directive defines the first atom of the
water molecule. The settle funct is always 1, and the distance between
O-H and H-H distances must be given. **Note** that the algorithm can
also be used for TIP3P and TIP4P 128. TIP3P just has
another geometry. TIP4P has a virtual site, but since that is generated
it does not need to be shaken (nor stirred).