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The distance between two atoms within the same [moleculetype]
can be restrained to a prescribed distance by setting [distance_restraints]
in the topology. Manual section 4.3.4 describes the implementation and underlying equations for this algorithm. An example [distance_restraints]
section (taken from the manual) might look like:
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
10 16 1 0 1 0.0 0.3 0.4 1.0
10 28 1 1 1 0.0 0.3 0.4 1.0
10 46 1 1 1 0.0 0.3 0.4 1.0
16 22 1 2 1 0.0 0.3 0.4 2.5
The above directive specifies distance restraints between pairs of atoms (ai
and aj
). The terms used are as follows:
type
: the only value is 1 index
: multiple restraints with the same index
value can be controlled together. Above, the second and third restraints are considered together, while the first and fourth are separate from this pair. type'
: the value can be 1 or 2; using 2 means the restraint will not be time- or ensemble-averaged (useful for restraining hydrogen bonds) low
: the value of r_{0} in equation 4.76 of the manual. See also Figure 4.13. up1
: the value of r_{1} in equation 4.76 and Figure 4.13 up2
: the value of r_{2} in equation 4.76 and Figure 4.13 fac
: the factor by which the force constant (disre_fc
in the .mdp file) is multiplied. In this way, different restraints can be maintained by different force constants, even though only one value of disre_fc
is given.