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Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin
International Tables for Crystallography (2012). Vol. F, ch. 20.1, pp. 633-641 [ doi:10.1107/97809553602060000877 ]
Chapter 20.1. Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin A unit cell of ubiquitin was simulated for 2ns using molecular dynamics to investigate the degree of convergence of different molecular properties in crystals. Energies, deviation from the experimentally derived crystal structure, atomic positional fluctuations and dihedral ...
Water diffusion
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 ...
[more results from section 20.1.3 in volume F]
Methods
International Tables for Crystallography (2012). Vol. F, Section 20.1.2, pp. 633-634 [ doi:10.1107/97809553602060000877 ]
Methods 20.1.2. Methods Ubiquitin consists of 76 amino acids with 602 non-hydrogen atoms. Hydrogen atoms attached to aliphatic carbon atoms are incorporated into these (the united-atom approach), and the remaining 159 hydrogen atoms are treated explicitly. Ubiquitin crystallizes in the orthorhombic space group , with a = 5.084, b = 4.277 and ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 20.1.1, p. 633 [ doi:10.1107/97809553602060000877 ]
Introduction 20.1.1. Introduction Molecules in crystals are often believed to have a very rigid structure due to their ordered packing, and the investigation of the molecular motion of such systems is often considered to be of little interest. In contrast to small-molecule crystals, however, the solvent concentration in protein crystals ...
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 20.1.4, p. 640 [ doi:10.1107/97809553602060000877 ]
Conclusions 20.1.4. Conclusions In the present molecular-dynamics simulation, fast convergence in energy, within about 100ps, was observed. Other properties, such as dihedral-angle fluctuations and backbone atom-position fluctuations, converged on an intermediate timescale of hundreds of picoseconds. Root-mean-square deviations of the simulated protein molecules from the starting ...
International Tables for Crystallography (2012). Vol. F, ch. 20.1, pp. 633-641 [ doi:10.1107/97809553602060000877 ]
Chapter 20.1. Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin A unit cell of ubiquitin was simulated for 2ns using molecular dynamics to investigate the degree of convergence of different molecular properties in crystals. Energies, deviation from the experimentally derived crystal structure, atomic positional fluctuations and dihedral ...
Water diffusion
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 ...
[more results from section 20.1.3 in volume F]
Methods
International Tables for Crystallography (2012). Vol. F, Section 20.1.2, pp. 633-634 [ doi:10.1107/97809553602060000877 ]
Methods 20.1.2. Methods Ubiquitin consists of 76 amino acids with 602 non-hydrogen atoms. Hydrogen atoms attached to aliphatic carbon atoms are incorporated into these (the united-atom approach), and the remaining 159 hydrogen atoms are treated explicitly. Ubiquitin crystallizes in the orthorhombic space group , with a = 5.084, b = 4.277 and ...
Introduction
International Tables for Crystallography (2012). Vol. F, Section 20.1.1, p. 633 [ doi:10.1107/97809553602060000877 ]
Introduction 20.1.1. Introduction Molecules in crystals are often believed to have a very rigid structure due to their ordered packing, and the investigation of the molecular motion of such systems is often considered to be of little interest. In contrast to small-molecule crystals, however, the solvent concentration in protein crystals ...
Conclusions
International Tables for Crystallography (2012). Vol. F, Section 20.1.4, p. 640 [ doi:10.1107/97809553602060000877 ]
Conclusions 20.1.4. Conclusions In the present molecular-dynamics simulation, fast convergence in energy, within about 100ps, was observed. Other properties, such as dihedral-angle fluctuations and backbone atom-position fluctuations, converged on an intermediate timescale of hundreds of picoseconds. Root-mean-square deviations of the simulated protein molecules from the starting ...
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