shake.def

The shake.def file provides constraints on residues and molecules in addition to the default constraints on bonded hydrogens. Thereby, one can ommit for example the awkward H--H bond for water, often found in psf files.

    ! the syntax is the follwing:
    !
    ! FIX_BOND RESNAME VALUE ATOMNAME ATOMNAME
    ! FIX_ANGL RESNAME VALUE ATOMNAME ATOMNAME ATOMNAME
    ! FIX_DIHE RESNAME VALUE ATOMNAME ATOMNAME ATOMNAME ATOMNAME
    ! 
    ! For VALUE, you can either use a numerical value or
    ! the D for DEFAULT statement to use the forcefield value

    FIX_BOND TIP3  D  H1 OH2
    FIX_BOND TIP3  D  H2 OH2
    FIX_BOND TIP3  D  H1 H2