string-g.in

colvar {
    name gs

    width                 0.01
    lowerboundary         0.0
    upperboundary         1.0
    lowerwallconstant     10.0
    upperwallconstant     10.0

    extendedLagrangian    on
    extendedFluctuation   0.01

    gspath {
        atoms {atomnumbers { 1 5 6 7 9 11 15 16 17 19 }}
        refPositionFile1 string-00.pdb
        refPositionFile2 string-01.pdb
        refPositionFile3 string-02.pdb
        refPositionFile4 string-03.pdb
        refPositionFile5 string-04.pdb
        refPositionFile6 string-05.pdb
        refPositionFile7 string-06.pdb
        refPositionFile8 string-07.pdb
        refPositionFile9 string-08.pdb
        refPositionFile10 string-09.pdb
        refPositionFile11 string-10.pdb
        refPositionFile12 string-11.pdb
        refPositionFile13 string-12.pdb
        refPositionFile14 string-13.pdb
        refPositionFile15 string-14.pdb
        refPositionFile16 string-15.pdb
        refPositionFile17 string-16.pdb
        refPositionFile18 string-17.pdb
        refPositionFile19 string-18.pdb
        refPositionFile20 string-19.pdb
    }
}

colvar {
    name gz
    width                 0.01
    lowerboundary         -99.0
    upperboundary         99.0
    gzpath {
        atoms {atomnumbers { 1 5 6 7 9 11 15 16 17 19 }}
        refPositionFile1 string-00.pdb
        refPositionFile2 string-01.pdb
        refPositionFile3 string-02.pdb
        refPositionFile4 string-03.pdb
        refPositionFile5 string-04.pdb
        refPositionFile6 string-05.pdb
        refPositionFile7 string-06.pdb
        refPositionFile8 string-07.pdb
        refPositionFile9 string-08.pdb
        refPositionFile10 string-09.pdb
        refPositionFile11 string-10.pdb
        refPositionFile12 string-11.pdb
        refPositionFile13 string-12.pdb
        refPositionFile14 string-13.pdb
        refPositionFile15 string-14.pdb
        refPositionFile16 string-15.pdb
        refPositionFile17 string-16.pdb
        refPositionFile18 string-17.pdb
        refPositionFile19 string-18.pdb
        refPositionFile20 string-19.pdb
    }
}

harmonic {
   colvars               gz
   centers               0.0
   forceConstant         0.5
}

abf {
   colvars               gs
   fullSamples           500
}