Gromacs

Distance Restraints

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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 r0 in equation 4.76 of the manual.  See also Figure 4.13.
    • up1: the value of r1 in equation 4.76 and Figure 4.13
    • up2: the value of r2 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.
    Page last modified 18:17, 18 Apr 2010 by JLemkul?