Gromacs

Dihedral Restraints

    Table of contents
    1. 1. Notes

    In GROMACS versions since 4.6, dihedral restraints are specified wholly in the topology. The mdp settings formerly used have been removed.

    In GROMACS version 3.3.1, the atomic specification of dihedral restraints is part of the topology file and force constants, etc. are specified in the .mdp file.

    So, assuming that you have atoms numbered like this in your peptide.itp

    C' (n-1) = 5
    N  (n)   = 7
    CA (n)   = 9
    C' (n)   = 15
    N  (n+1) = 17
    

    Then you would use a section like this in your .top file, where 180 is replaced by the actual dihedral value (in degrees) to which you want to restrain the atoms.

    #include "peptide.itp"
    [ dihedral_restraints ]
    ; ai   aj    ak    al  type  label  phi  dphi  kfac  power
    ; phi C'(n-1) - N - CA - C'
        5    7     9    15     1      1  180     0     1      2
    ; psi N - CA - C' - N(n+1)
        7    9    15    17     1      1  180     0     1      2
    
    #include "tip3p.itp"
    ;etc...
    

    Make sure that the dihedral_restraints section comes immediately after the inclusion of the protein topology (.itp file). If you have the protein topology directly in your .top file then just insert dihedral_restraints after the protein listing but before any mention of things that are not that protein molecule.

    The implementation of dihedral restraints is described in section 4.3.3 of the manual.  The parameters specified in the [dihedral_restraints] directive are as follows:

    • type: the only value is 1
    • label: unused, and has been removed from the code for upcoming versions
    • phi: the value of φ0 in equations 4.74 and 4.75 of the manual
    • dphi: the value of Δφ in equation 4.75 of the manual
    • kfac: analogous to fac in the implementation of distance restraints, the factor by which the force constant (specified in the .mdp file, see below) is multiplied.  By doing so, different restraints can be maintained with different force constants, even though only one value of dihre_fc is supplied.
    • power: unused, and has been removed from the code for upcoming versions

     

    Notes

    1. The dihedral restraints either work differently in version 3.3 or they are broken; use GROMACS version 3.3.1 (Mobley, Chodera and Dill, J. Chem. Phys. 125, 084902 (2006), page 084902-6, section III D.)

    2. The manual is a bit unclear about whether this type of dihedral restraint is stable for use near 180 degrees. Chris Neale has found that everything appears to behave normally and as expected over the entire range of dihedral angles including 180 degrees. However, one must avoid the situation in which the actual dihedral is close to 180deg away from the restrained dihedral.

    2b. Not everybody agrees with part 2 (above). See for instance, see here. Therefore the user is asked to please do some tests to draw your own conclusions.

    3. Take special care of units. Quoting GROMACS Manual version 3.3 page 58 "Note that in the input in topology files, angles are given in degrees and force constants in kJ mol-1 rad-2.

    Page last modified 08:59, 15 Sep 2017 by mabraham