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. Author manuscript; available in PMC: 2013 Aug 14.
Published in final edited form as: J Chem Theory Comput. 2012 Jul 5;8(8):2581–2587. doi: 10.1021/ct3002046

Table 1.

Recursive, base-to-tip algorithms for converting between the θ. and v coordinates using Eq. 33 for serial-topology systems.

v=D12[I+HϕK]θ. θ.=[IHψK]D12v

             V(N+1)=0              V(N+1)=0
fork=N1 fork=N1
     V+(k)=ϕ(k+1,k)V(k+1)      V+(k)=ϕ(k+1,k)V(k+1)
         v(k)=D12(k)[θ.(k)+G(k)V+(k)]          θ.(k)=D12(k)v(k)G(k)V+(k)
         V(k)=V+(k)+H(k)θ.(k)          V(k)=V+(k)+H(k)θ.(k)
end loop end loop