1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
|
.. _constraintalg:
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. :ref:`excl`).
The distances are constrained using the LINCS or the SHAKE algorithm,
which can be selected in the :ref:`mdp` file. Both types of constraints can be
perturbed in free-energy calculations by adding a second constraint
distance (see :ref:`constraintforce`). Several types of bonds and
angles (see :numref:`Table %s <tab-topfile2>`) can be converted automatically to
constraints by :ref:`grompp <gmx grompp>`. There are several options for this in the :ref:`mdp`
file.
We have also implemented the SETTLE
algorithm \ :ref:`47 <refMiyamoto92>`, 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 \ :ref:`128 <refJorgensen83>`. TIP3P just has
another geometry. TIP4P has a virtual site, but since that is generated
it does not need to be shaken (nor stirred).
|
