SPC waters

Figure 2 Pair correlation functions of 0-0 and O-H at ( puted with the parameters of the SPC water model.

Fig. 5. Probabilities pn of observing n water-oxygen atoms in spherical cavity volumes v. Results from Monte Carlo simulations of SPC water are shown as symbols. The parabolas are predictions using the flat default model in Eq. (11). The center-to-center exclusion distance d (in nanometers) is noted next to the curves. The solute exclusion volume is defined by the distance d of closest approach of water-oxygen atoms to the center of the sphere. (Hummer et al., 1998a)... 

Figure 5 shows pn distributions for spherical observation volumes calculated from computer simulations of SPC water. For the range of solute sizes studied, the In pn values are found to be closely parabolic in n. This result would be predicted from the flat default model, as shown in Figure 5 with the corresponding results. The corresponding excess chemical potentials of hydration of those solutes, calculated using Eq. (7), are shown in Figure 6. As expected, /x x increases with increasing cavity radius. The agreement between IT predictions and computer simulation results is excellent over the entire range d < 0.36 nm that is accessible to direct determinations of po from simulation.

Fig. 6.11. The error in the free energy measured by several NEW implementations. Results are from Monte Carlo simulations of ion charging in water at 298 K. System 0 consists of a single Lennard-Jones atom with charge of +le and 216 SPC water molecules, and system 1 is the same but with the charge turned off. One work cycle contains 100 nonuniform steps in 7 from 0 to 1 and back. For a detailed description of the simulation, see [43]...

Fig. 9.5. Plot of ln[ 2Q.(s)/ 0)(e)]. The region between —2.5kcalmol 1 and - 0.5 kcal moP1 is satisfactorily linear, and (9.17) yields T w 302 K, in good agreement with the simulation temperature of 298 K. The intercept gives //ex =2.5 kcal mol-1 in agreement with a value of 2.5 kcalmoP1 for the SPC water model [63]...

As a simple example of a QM/MM Car-Parinello study, we present here results from a mixed simulation of the zwitterionic form of Gly-Ala dipeptide in aqueous solution [12]. In this case, the dipeptide itself was described at the DFT (BLYP [88, 89 a]) level in a classical solvent of SPC water molecules [89b]. The quantum solute was placed in a periodically repeated simple cubic box of edge 21 au and the one-particle wavefunctions were expanded in plane waves up to a kinetic energy cutoff of 70 Ry. After initial equilibration, a simulation at 300 K was performed for 10 ps. 

Allen and Bevan (80) have applied the SMD technique to the study of reversible inhibitors of monoamine oxidase B, and this paper will be used as an example for discussion of the constant velocity SMD pulling method. They used the Gromacs suite of biomolecular simulation programs (18) with the united-atom Gromos 43al force field to parameterize the lipid bilayer, protein, and small-molecule inhibitors. The protein was inserted into their mixed bilayer composed of phosphatidyl choline (POPC) and phosphatidyl ethanolamine (POPE) lipids in a ratio known to be consistent for a mitochondrial membrane. Each inhibitor-bound system studied was preequilibrated in a periodic box of SPC water (20) with the simulations run using the NPT ensemble at 300 K and 1 atm pressure for 20 ns. Full atomic coordinates and velocities were saved in 200-ps increments giving five replicates for each inhibitor-bound system. A dummy atom was attached to an atom (the SMD atom shown in Fig. 7) of the inhibitor nearest to the... 

FIGURE 5.1. Liquid/vapour coexistence curves of SPC water (solid line) and OPLS methanol (dashed line) following hrom the RISM-KH theory. Molecular simulation results for water [45] and methanol [46] (open circles and squares, respectively) and critical point extrapolations (filled symbols). 

Pterin cation, TIP3, and SPC water van der Waals parameters... 

A different approach is that followed by Aqvist [190], who determines the parameters of the short range part of the potentials of alkaline and alkaline earth ions in SPC water by matching calculated and observed free energies of hydration. According to Aqvist, this approach is more reliable than that based on relative free energies [191-195]. 

Figure 47. Diffusion coefficient for SPC water in the vicinity of a protein. The diffusion coefficient is plotted versus the distance (in A) of the water molecule center of mass from the surface of trypsin. (From Ref. 340.)...

To study the vibrational energy relaxation of the amide I mode in N-methylacetamide, we employed the OPLS all-atom force field to model the solute and the flexible simple-point-charge (SPC) water modeF with doubled hydrogen masses to model the solvent D2O. To investigate the photoinduced heat transfer in photoswitchable peptides, we used the GROMOS96 united atom force field 43al. Additional force field parameters for the azobenzene unit were derived from density functional theory as described in Ref. [32]. We employed a united-atom modeP to describe the DMSO solvent, the SPC modeP to describe water, and the rigid all-atom model of Ref [57] to describe the chloroform solvent. 

Liquid water is an important medium in which most biomolecules perform their function. Pure liquid water may seem like a very simple system, where one may be able to identify the determining factors of its properties easily, but this is not always found to be the case. Table 2 gives examples of studying several thermodynamic properties of liquid water using a flexible SPC water model in a molecular dynamics simulation. This flexible water model was characterized by the following interaction potential ... 

Table 2. The Most Significant Parameters of the Flexible SPC Water Model That Control Different Thermodynamic Properties of Liquid Water ... 

Figure 1.18. Pressure isotherms of SPC water (solid lines) obtained by the RISM/KH theory supplemented with the Maxwell construction. Metastable and unstable states (thin solid and short-dash portions, respectively). Binodal and spinodal (bold solid and dashed lines, respectively).

Figure 1.19. Liquid-vapor coexistence line of SPC water and OPLS methanol (solid and dashed lines) following from the RISM/KH theory versus the simulation data (open circles and squares, respectively) and critical point estimates (closed symbols). Logarithmic and linear scales are used to resolve the density in gas and liquid state.

Figure 1.19 draws a comparison between the predictions of the RISM/KH approach and the simulation data for the liquid-vapor coexistence envelopes of SPC water [107] and OPLS-UA methanol [108]. The theory qualitatively reproduces the phase diagrams. Remarkable is a good fit for their vapor branches. The predicted critical temperature of water,... 

A microscopic part of a monolayer consisting of monododecylpentaethylene glycol surfactants (C12E5) adsorbed at the water surface was simulated with the AMBER force field and the SPC water parameter set (5). The temperature T was set to 298 K, while the number of molecules, A, was composed of 36 surfactant and 1575 water molecules arranged in a cubic box with periodic boundary conditions. The area per surfactant molecule (A) corresponded to a value of A = 0.55 nm, which is somewhat larger than the critical micelle concentration (CMC) of C]2E5 (A = 0.50 0.03 nm ). 

Fig. 8.3 Free energy profiles along the S-S -C-C dihedral angle of the disulfide bridge of the 127 protein as a function of external force. The profile has been obtained from force-field molecular dynamics simulations carried out with GROMOS at r = 300 K. The model system in these simulations comprises the 127 protein and SPC water molecules solvating the protein in a tetragonal box. The relevant S-S-C-C conformers of the disulfide bridge embedded in the protein are shown on top using a partial and schematic representation. Courtesy of Padmesh Anjukandi...

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