Ways to Speed up the Calculations

A second idea to save computational time addresses the fact that hydrogen atoms, when involved in a chemical bond, show the fastest motions in a molecule. If they have to be reproduced by the simulation, the necessary integration time step At has to be at least 1 fs or even less. This is a problem especially for calculations including explicit solvent molecules, because in the case of water they do not only increase the number of non-bonded interactions, they also increase the number of fast-moving hydrogen atoms. This particular situation is taken into account 

It is important to notice that the united-atom simplification cannot be applied to functional hydrogens which are involved in the formation of a hydrogen hond or a salt bridge. This would destroy interactions important for the structural integrity of the protein. Removing the hydrogen at the u-carbon of the peptide backbone is also dangerous, because it prevents racemization of the amino acid. 

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This term is, however, usually smaller than the error in the DFT calculations of the FC term. And, since the calculations of the SD terms are the most expensive part of the nuclear spin-spin coupling constant calculations using the DFT approach (so far we have not found a way to speed up the calculation of this term), it is therefore neglected in the present approach. 

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