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In the GROMACS code modifications, instead of the nanometer unit for the distance that is standard in GROMACS, a unit of 1 A was previously assumed. This led to dipole-dipole interactions between amide I vibrations at different sites and the interaction energies of the amide I vibration with the protein hydrogen bonds being overestimated, respectively, by three orders and by one order of magnitude. In addition, the quantum mechanical force terms were overestimated because, through the same error, the sites defined as hydrogen-bonded in the protein were not properly identified. Because the influence of the quantum vibration on the conformation of the polypeptide is less pronouncedwhen these errors are corrected, the simulation times are increased to 10 ps. Moreover, each of the 20 simulation runs, obtained by varying the seed of the random number generator for the initial velocities, was repeated ten times in order to sample different quantumMonte Carlo paths and to yield better statistical estimates. Thus, the results presented here, for each value of χ , represent averages over 200 simulation trajectories. Two other changes are made in the current modified GROMACS code. The first of these makes sure that the interaction energy term varies continuously with the length of the hydrogen bond, even when the hydrogen bond breaks. This term is calculated as

Adenosine triphosphate (ATP) is known to be the main energy currency of the living cell, and is used as a coenzyme to generate energy for many cellular processes through hydrolysis to adenosine diphosphate (ADP), although the mechanism of energy transfer is not well understood. It has been proposed that following hydrolysis of the ATP cofactor bound to a protein, up to two quanta of amide-I vibrational energy are excited and utilized to bring about important structural changes in the protein. To study whether, and how, amide-I vibrational excitations are capable of leading to protein structural changes, we have added components arising from quantum-mechanical amide-I vibrational excitations to the total energy and force terms within a molecular-dynamics simulation. This model is applied to helical deca-alanine as a test case to investigate how its dynamics differs in the presence or absence of an amide-I excitation. We find that the presence of an amide-I excitation can bias the structure toward a more helical state.