relaxed dihedral scans with namd

In case you want to perform a relaxed scan of the potential energy surface for a given dihedral, you have to perform constrained (or at least restrained) optimizations. The namd way to do so is to define a collective variable (colvar in namd terminology) and then impose a harmonic potential on this collective variable. Please note that namd only supports restraints but no constraints during energy minimization.

namd requires only little input: first of all, colvar calculation has to be enabled by adding two lines to your job configuration file.

colvars on
colvarsConfig colvars.conf

The second line introduces a separate configuration file with a different syntax. For a dihedral of the atoms 12, 3, 4, 15 it should look similar to:

colvar {
    name dih # user defined name that appears in the optional output and is necessary for references

    outputValue on # writes a trajectory of the colvar to the logfile.

    dihedral {
        group1 {
            atomNumbers 12
        }
        group2 {
            atomNumbers 3
        }
        group3 {
            atomNumbers 4
        }
        group4 {
            atomNumbers 15
        }
    }
}

harmonic {
    name dih_pot # arbitrary
    colvars dih # unique reference
    centers -50 # desired value
    forceConstant 5.0 # well, ...
}

Please note that the atom numbers are counted from one.