Constraint algorithms

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).