• Jason Swails's avatar
    Add NBFIX support to the Amber topology file parsers. The new Amber ff14IPQ · d865c202
    Jason Swails authored
    force field utilizes nbfix functionality. Without this commit, using a ff14IPQ
    topology file (or one modified by ParmEd to contain off-diagonal LJ elements),
    would happily run, but ignore off-diagonal elements.
    
    The new Chen and Garcia RNA force field (see doi:10.1073/pnas.1309392110) also
    utilizes off-diagonal terms in its parametrization scheme.
    
    One shortcoming is that the approach taken here -- using a pair parameter lookup
    table -- cannot be currently used with a long-range correction because it is not
    a `Continuous1DFunction' by virtue of using two `Discrete2DFunction'
    TabulatedFunction classes.
    
    Energies here match the values obtained with Amber to 0.01 -- 0.1 kcal/mol
    (within 0.1% of the total).
    d865c202
ff14ipq.rst7 99.8 KB