Study On Molecular Dynamics Simulations Of Liquid Water And Molecule Electronegativity Of Polypeptides And Protein

Molecular dynamics simulations of liquid water were run in this paper using ABEEM-7Pwater model, first we studied the changes of temperature and pressure at298K,1atm withBerendsen coupling method,then we found the appropriate τT=0.01ps and τP=0.05ps. Basedon the average temperature and pressure calculated at different temperatures and1atm, wevalidated the reasonableness of τTand τP. We also computed the average, minimum andmaximum charge of sites in liquid water system containing216and500water molecules atdifferent temperatures in NVT ensemble and NPT ensemble. Via comparing the averagecharge, we found that the average value of charge at same site had little difference among thedifferent temperatures. Relatively speaking, there was more positive charge on O and H atomsof larger system in NVT ensemble and less negative charge on the lone pair of O atom andO-H bond. In contrast to the results of the same system under NVT ensemble and NPTensemble, the polarization of NVT ensemble was slightly stronger than the NPT ensemble.In order to understand the nature of the charge and molecule electronegativity calculationusing ABEEM, the electronegativities of several neutral polypeptides and protein1CRN werecalculated in this paper using ABEEMσπ method. Through the comparison, we found that theelectronegativity of cysteine dipeptide was maximum among eleven neutral dipeptides, theminimum electronegativity happened to be on tryptophan dipeptide. For tetrapeptides in fiveconformations (left-handed helix, right-handed helix, β-sheet, antiparallel βa-sheet andpolyproline II), the maximum electronegativity of same kind conformation (e.g. left-handedhelix) was always on cysteine tetrapeptide and the minimum was always on tryptophantetrapeptide. The electronegativity of protein1CRN was slightly less than the polypeptides. Inthis paper, we also calculated arithmetic mean value, geometric mean value and harmonicmean value of the preceding two items added in the effective electronegativity calculationformula of all sites in molecule, we found that the electronegativities of chosen moleculesafter equilibrium were close to the arithmetic mean value mostly, the absolute deviation didn’texceed0.1000ev. This meant that in subsequent calculations, we can estimate all the chargeof sites in molecule then estimate the molecule equilibrium electronegativity, finally simplifyABEEMσπ method.