All- proteins simplified by NHP model with its secondary structure information were studied by molecular dynamics simulation.The transitions of potential energy in 50 all- proteins under different temperatures were well discussed in this paper.It is concluded that the bond-stretching and bending energies increase linearly with the chain length.The bond-stretching and bending energies of each bond also increase linearly with the temperature due to more obvious bond vibration under high temperatures.The slope of the linear relationship between bond-stretching energy and temperature is larger than the one of bond-bending energy as the function of T*.The bond-torsional energy decreases linearly with the number of -helix in each protein chain

instead of the chain length.It increases with the temperature when the temperature is lower than 0.3.And then it decreases with the temperature increasing.Non-bond energy is mainly dependent on hydrophobic-hydrophobic interactions.It doesn't show obvious linear relationship due to the mutual interactions between hydrophilic

hydrophobic

or neutral residues.The transition temperatures are shown in bond-torsional and non-bond potential energies.The native structure is related to the mutual effect of bond and non-bond potential energies

which compete with each other for lower potential energy.These conclusions provide a natural realization of understanding the structure of proteins.