Structural and dynamic properties of SPC/E water

Abstract

I have investigated the structural and dynamic properties of water by performing a series of molecular dynamic simulations in the range of temperatures from 213 K to 360 K, using the Simple Point Charge-Extended (SPC/E) model. I performed isobaric-isothermal simulations (1 bar) of 1185 water molecules using the GROMACS package. I quantified the structural properties using the oxygen-oxygen radial distribution functions, order parameters, and the hydrogen bond distribution functions, whereas, to analyze the dynamic properties I studied the behavior of the history-dependent bond correlation functions and the non-Gaussian parameter α2(t) of the mean square displacement of water molecules. When the temperature decreases, the translational (τ ) and orientational (Q) order parameters are linearly correlated, and both increase indicating an increasing structural order in the systems. The probability of occurrence of four hydrogen bonds and Q both have a reciprocal dependence with T , though the analysis of the hydrogen bond distributions permits to describe the changes in the dynamics and structure of water more reliably. Thus, an increase on the caging effect and the occurrence of long-time hydrogen bonds occur below ∼ 293 K, in the range of temperatures in which predominates a four hydrogen bond structure in the system.

How can we detect hydrogen bond local cooperativity in liquid water: A simulation study

“…We carried out a detailed analysis of the H-bonding properties of the nine investigated systems. The number of average H-bonded neighbor number (nhb) decreases as a function of temperature being in good agreement with other studies [43][44][45][46][47][48] (see Table 1.). Interestingly, in contrast to previous assumptions the H-bond definition affects this quantity considerably, as the more restrictive energetic definition yields on average 0.5 unit smaller nhb values than the geometric definition.…”

Structural basis of βTrCP1-associated GLI3 processing

“…All MD simulations were performed by GROMOS96 43a1 force field 32 to acquire the equilibrated system. All systems were solvated using SPC water model 33 in a periodic box, followed by the addition of Na + and Cl − counter ions to neutralize the system. Before MD simulations, systems were subjected to energy minimization to remove initial steric clashes using 1000 steps of steepest descent algorithm via a tolerance of 10 KJ/mol/nm −1 .…”

Comparison of different computational methods for water structure optimisation

“…Perhaps, as the most common solvent in the nature is essential for human being. The properties of water, like the heat of vaporisation, the self diffusion coefficient, the atom-atom pair distribution function, the temperature of maximum density, the critical parameters, the dielectric constant and many others have been intensively studied by physical experiments as well as computer simulations , Campo, 2010, Head-Gordon, 2002, Tunon et al 1996. The choice of a computational technique plays an essential role in all numerical experiments.…”