How does the Electrostatic Force Cut-Off Generate Non-uniform Temperature Distributions in Proteins?

Abstract

Molecular dynamics simulations (MDS) with electrostatic force cut-off on heterogeneous molecular systems make temperature separation between solute and solvent [1 –4]. In MDS where the temperature separation occurs, we found that there is a non-uniform temperature distribution in protein. The pattern of temperature distribution was shown to be peculiar to the protein, suggesting a possible relationship between dynamical and thermal properties of protein. By principal component analysis, the non-uniform temperature distribution was ascribed to high temperature of large fluctuation modes in protein. Further analysis by thermal diffusion equation between principal modes showed that in protein large fluctuation modes inherently have smaller value of heat capacity than small fluctuation modes have and are easily heated up by truncation noise due to abrupt cut-off of electrostatic forces.