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 Results for DC.creator="U." AND DC.creator="Stocker" in section 20.1.3 of volume F
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Stocker, U. and Gunsteren, W. F. van  International Tables for Crystallography (2012). Vol. F, Section 20.1.3, pp. 634-640 [ doi:10.1107/97809553602060000877 ]
Results 20.1.3. Results 20.1.3.1. Energetic properties | | In Fig. 20.1.3.1, the non-bonded contributions to the total potential energy are shown. The non-bonded interactions comprise Lennard-Jones and electrostatic interactions. Solvent-solvent, solute-solute and solute-solvent interaction energies are shown separately. All of these appear converged after approximately 100ps. The ...

Dihedral-angle fluctuations and transitions
Stocker, U. and Gunsteren, W. F. van  International Tables for Crystallography (2012). Vol. F, Section 20.1.3.6, pp. 639-640 [ doi:10.1107/97809553602060000877 ]
Dihedral-angle fluctuations and transitions 20.1.3.6. Dihedral-angle fluctuations and transitions Backbone dihedral-angle fluctuations and transitions are examined in Tables 20.1.3.3 and 20.1.3.4 using different analysis periods. After the first 400ps of analysis, the dihedral-angle fluctuations differ only slightly, but if longer averaging times are chosen, the different protein ...

Internal motions of the proteins
Stocker, U. and Gunsteren, W. F. van  International Tables for Crystallography (2012). Vol. F, Section 20.1.3.5, p. 639 [ doi:10.1107/97809553602060000877 ]
Internal motions of the proteins 20.1.3.5. Internal motions of the proteins Fig. 20.1.3.8 displays the atomic root-mean-square position fluctuations for the C[alpha] atoms of the four protein molecules during the whole analysis period, together with corresponding values obtained using equation (20.1.3.1) and the crystallographic B factors. Rotational and ...

Effect of the averaging period
Stocker, U. and Gunsteren, W. F. van  International Tables for Crystallography (2012). Vol. F, Section 20.1.3.4, pp. 638-639 [ doi:10.1107/97809553602060000877 ]
Effect of the averaging period 20.1.3.4. Effect of the averaging period In Fig. 20.1.3.6, we concentrate again on molecule 4. Comparing different averaging periods of 400 and 800ps with different starting points, it can be seen that, in general, the later the simulation, the less motion observed. During the period 800 ...

Effect of the translational and rotational fitting procedure
Stocker, U. and Gunsteren, W. F. van  International Tables for Crystallography (2012). Vol. F, Section 20.1.3.3, pp. 636-638 [ doi:10.1107/97809553602060000877 ]
Effect of the translational and rotational fitting procedure 20.1.3.3. Effect of the translational and rotational fitting procedure In Fig. 20.1.3.4, the impact of different fitting protocols on atomic mean-square position fluctuations (RMSFs) is examined. B factors are related to mean-square position fluctuations according to where the angle brackets indicate ...

Structural properties
Stocker, U. and Gunsteren, W. F. van  International Tables for Crystallography (2012). Vol. F, Section 20.1.3.2, pp. 634-636 [ doi:10.1107/97809553602060000877 ]
Structural properties 20.1.3.2. Structural properties Not all properties converge as fast as the energies. Fig. 20.1.3.2 shows the root-mean-square atom-position deviation (RMSD) from the X-ray structure for each of the four individual chains for both C[alpha] atoms and all atoms. Here, several relaxation periods can be ...

Energetic properties
Stocker, U. and Gunsteren, W. F. van  International Tables for Crystallography (2012). Vol. F, Section 20.1.3.1, p. 634 [ doi:10.1107/97809553602060000877 ]
Energetic properties 20.1.3.1. Energetic properties In Fig. 20.1.3.1, the non-bonded contributions to the total potential energy are shown. The non-bonded interactions comprise Lennard-Jones and electrostatic interactions. Solvent-solvent, solute-solute and solute-solvent interaction energies are shown separately. All of these appear converged after approximately 100ps. The solvent ...

Water diffusion
Stocker, U. and Gunsteren, W. F. van  International Tables for Crystallography (2012). Vol. F, Section 20.1.3.7, p. 640 [ doi:10.1107/97809553602060000877 ]
Water diffusion 20.1.3.7. Water diffusion In Fig. 20.1.3.9, the number of water oxygen atoms with a given atomic root-mean-square position fluctuation (RMSF) are plotted. The time evolution and the shapes of these curves are similar to those obtained for bulk water, a Gaussian distribution with the maximum at larger ...

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