Structure and dynamics of liquid water with different long‐range interaction truncation and temperature control methods in molecular dynamics simulations

Abstract

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.

Effect of Surface Polarity on the Structure and Dynamics of Water in Nanoscale Confinement

“…Our D Bulk , obtained from a MD simulation of bulk water at the same thermodynamic conditions, is 28% higher than that reported in the literature for SPC/E, 2.5 × 10 -5 cm 2 s -1 at 306 K and 0.998 g cm -3 , and 33% higher than the experimental diffusion coefficient of water, 2.4 × 10 -5 cm 2 s -1 at 300 K. 39 It is known that the system size, interaction truncations, and long-range interaction schemes (e.g., reaction field and Ewald sums) affect the structure and dynamics of simulated water. 40,49 For example, values as high as 4.4 × 10 -5 cm 2 s -1 have been reported for SPC/E water using the Ewald sum method. 50 Since the value reported by Berendsen et al 39 was obtained applying a spherical cutoff for long-range interactions in a smaller system than ours (216 SPC/E water molecules in Berendsen's work compared to 729 in our bulk simulations), where we use the Ewald summation, we deem it appropriate to attribute the discrepancy in D to differences in system size and method of truncation.…”

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

“…91 The diffusion constants for pure water by the Drude and SPC/E water models were close to the experimental value while additive TIP3P water model overestimated the values by a factor of two, as previously reported. 95 All models overestimate the diffusion constant for NMA, with the Drude FF producing the smallest difference. It should be noted that the system size correction for diffusion constant calculations suggested by Yeh et al 75 was adopted in the present study.…”

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

“…The initial structure of the DNA double helix was built using the NAB package [67] with idealized B-DNA structure parameters. The simulation software was the Gromacs package [68,69] with the CHARMM27 force field [70,71] using the simple point charge model of water TIP3P [72][73][74]. The dimension of the cubic simulation cells was set to 90 Å.…”