1. 19 Mar, 2015 1 commit
  2. 11 Jul, 2014 1 commit
    • 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
  3. 01 Aug, 2013 1 commit
  4. 18 Nov, 2011 1 commit