Root mean square deviation RMSD

The differences between ab initio and molecular mechanics generated dipole moments were discussed. The MM3(2000) force field is better able to reproduce experimental dipole moments for a set of forty-four molecules with a root mean squared deviation (rmsd) of 0.145 Debye compared with Hartree-Fock (rmsd 0.236 Debye), M0ller-Plesset 2 (rmsd 0.263 Debye) or MM3(96) force field (rmsd 0.164 Debye). The orientation of the dipole moment shows that all methods give comparable angle measurements with only small differences for the most part. This consistency within methods is important information and encouraging since the direction of the dipole moment cannot be measured experimentally. 

Chapter 18 - The determination region of solubility of methanol with gasoline of high aromatic content was investigated experimentally at temperature of 288.2 K. A type 1 liquid-liquid phase diagram was obtained for this ternary system. These results were correlated simultaneously by the UNIQUAC model. By application of this model and the experimental data the values of the interaction parameters between each pair of components in the system were determined. This revealed that the root mean square deviation (RMSD) between the observed and calculated mole percents was 3.57% for methylcyclohexane + methanol + ethylbenzene. The mutual solubility of methylcyclohexane and ethylbenzene was also demostrated by the addition of methanol at 288.2 K. 

Moreover, the objective function obtained by minimizing the square of the difference between the mole fractions calculated by UNIQUAC model and the experimental data. Furthermore, he UNIQUAC structural parameters r and q were carried out from group contribution data that has been previously reported [14-15], The values of r and q used in the UNIQUAC equation are presented in table 4. The goodness of fit, between the observed and calculated mole fractions, was calculated in terms RMSD [1], The RMSD values were calculated according to the equation of percentage root mean square deviations (RMSD%) ... 

The rule of thumb for a successful application of molecular replacement is that the model should have a root-mean-square deviation (RMSD) on C-alpha coordinates 2.0-2.5 Angstroms with the target structure, corresponding to a sequence identity with the target of 25-35%. In practice, however, there are many more structures solved by MR in the PDB using models with sequence identity of 60% or higher than otherwise. 

One of the simplest methods is the comparison of the initial structure of the macromolecule to that throughout the trajectory via a distance measure such as the root mean square deviation (RMSD). This method is most informative for a system like a folded protein under native conditions, where the molecule is expected to spend the vast majority of the time in conformations quite similar to the crystal structure. If one computes the RMSD time series against the crystal structure, one expects to see a rapid rise due to thermal fluctuations, followed by a long plateau or fluctuations about a mean at longer timescales. If the RMSD... 

Table 8.2 Root mean square deviation (RMSD) of the backbone of the aligned models of the h AR. The main difference among the models is due to the loops, which represent the most variable region of the templates and consequently of the models. Particular attention has to be given to EL2 because it is part of the binding pocket and it can directly interact with ligands...

A root-mean-square deviation (RMSD) analysis of the amide backbone atoms is often a strong indicator of conformational changes of a protein in solution. An RMSD example is shown in Fig. 4, once again of G17(l-6) in DMSO. Periods of conformational stability are indicated by stretches in which the RMSD does... 

At the end of the equilibration protocol, a 3D-QSAR equation with a good correlation (r = 0.81) and a low root mean square deviation (rmsd 0.85) on the estimated interaction energies were derived. The predictive power of the model was evaluated with a test set of 11 taxanes and epothilones, obtaining a prediction coefficient of 0.78. 

To illustrate the consistency between the two programs, data for the ethanol-water system reported by Rieder and Thompson (11) were used. The first program estimated the values of the energy parameters and calculated the vapor-phase composition, y, with a root mean square deviation (RMSD) of 0.00847. The mean arithmetic deviation between the... 

Root-mean-square deviation (RMSD) of the coordinates of backbone atoms in the simulated structure from those in the X-ray crystal structiue of BChE. nonpre and pre refer to the non-prereactive and prereactive BChE-cocaine complexes, respectively... 

Tables Summary of the MD-simulated and optimized key distances (A) and the root-mean-square deviation (RMSD) of the simulated structures from the initial structure [115]...

Table 5 A comparison between quantum-mechanical and force-field treatment of dispersion and repulsive contributions to the free energy of solvation. The force field is given under method, and for each solvent the first line gives the root mean square deviation (rmsd, in kcal/ mol) and the second line gives the coefficient c that gives the best fit of y = cx with y being the force-field results and x being the quantum-mechanical results. All results are from ref 30...

Results of Calculatious. The root-mean-square deviations (rmsd) of the calculated pressures with respect to the experimental ones are listed in Tables 3 and 4. The comparison of the rmsd for alcohol/water mixtures indicates that the new equations provide the best performances for 29 VLF and NRTL for 5 sets. A similar conclusion was reached for the systems containing benzene, hexafluorobenzene, toluene, and cyclohexane the new equations provide the best performances for 7 sets, and the new equations and the NRTL provide almost the same results for 2 sets. 

Table 3. Root mean square deviation (RMSD) and maximum absolute deviation (MAD) of the total energy in 10 a.u. (see text for a definition) from a reference BLYP potential energy landscape of 25 configurations of 64 H2O for a variety of methods...

Another measure of the native state similarity is the root mean square deviation (RMSD) with respect to a reference (native) state given by... 

In the dRT-C-Mg simulation involving the activated precursor with Mg2 initially placed at the C-site, the Mg2+ ion quickly (<200 ps) migrates into the B-site position, as observed in a previous simulation study [44], and afterward exhibits nearly identical behavior as if the Mg2+ ion was initially placed at the B-site (dRT-B-Mg). Hence, we only extended the dRT-B-Mg simulation to 300 ns and designate it simply as dRT-Mg. All five simulations were carried out to 300 ns in a background of 0.14 M NaCl. The equilibration for each simulation was monitored by the root mean square deviation (RMSD) and was observed to reach a steady state after 30-50 ns. Hence, all analyses were performed over the last 250 ns of trajectories for each simulation. 

---