Thermodynamic Tables, Bibliography, and Property File. Sections VII, VIII, and IX
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The information; is federal and can develop combined with conservation described during cellular remains. In this invention, one genome is to another, which is molecules. The insertion boxes and unit cells are always described by parallelepipeds. The selection of the initial positions of particles inside an insertion box is made either using i a lattice or ii random numbers.
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The former approach involves a division of the insertion box into unit cells in all three dimensions see Fig. The particles are placed in the unit cells according to the symmetry of the lattice type specified by the user. The lattice symmetries available include primitive cubic, body centered cubic, and face centered cubic symmetry, but other cubic lattices of other symmetry are also available.
A large set of different possibilities to generate random initial configurations is available. The choice depends primarily on the type of objects present chains, hierarchical structures, or networks. The choice of initial particle coordinates affects the equilibration time, but normally not the outcome of the production run. For a disordered system, a random initial configuration is preferred due to shorter equilibration time.
However, for dense systems a regular initial configuration is often necessary as the random approach might fail at high density. Two options are available for generating initial velocities. They could either i be set to zero or ii initiated according to the Maxwell—Boltzmann distribution. As thermal equilibration of particle velocities is fast, the practical difference between these two options is small. Finally, the MC method is more robust than the MD method for equilibrating systems prepared far from equilibrium.
Hence, MD production runs of more complex systems can preferentially be equilibrated using the MC method. The switch from an equilibration using the MC method to a subsequent production run using the MD method is trivial. For the MD method, additional specifications include choice of integration algorithm, time step, initiation of velocities, and coupling to external temperature and pressure bath. As to the MC method, a number of different types of trial move are available, such as i translational and rotational move of single particles, ii pivot rotation of subchains, iii translation of chains, iv slithering move of chains, v charge change, vi volume change, and vii change of the number of particles.
Many of the trial moves can be combined with cluster moves, for which also nearby particles are subjected to the same trial move. This is useful for particles strongly coupled to neighboring particles. Finally, for the BD method, the specification only involves time step and diffusion coefficients in the absence of interaction.
The simulation time is normally reduced by only evaluating the force on a particle MD, BD or the potential energy MC involving a subset of all particles. The update of the neighbor list can be selected to appear at a given frequency or to be automatically controlled by the motion MD, BD or translation movement MC of the particles.
Three options for handling neighbor lists are available, see Table 4. The Verlet neighbor list is suitable for systems, whose extension does not grossly exceed the range of the nonbonded potential. Although not scientifically important, averages of a number of control quantities can be evaluated and written to the output file. The control quantities can provide further insight into the simulated system and potentially alert the user that the simulation is not proceeding in an appropriate way.
If invoked, such averages are written after each macrostep and grand averages are written after the simulation.
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The current set of control quantities comprises force, torque, linear moment, angular moment, translational temperature, rotational temperatures, all applicable to MD, and extensive statistics on the outcome of different trial moves applicable to MC. In addition, averages of particle displacement, orientation, and position are available. Fundamental thermodynamic quantities such as average energies, temperature, pressure, volume, and number of particles are considered as main quantities.
A more detailed list of main quantities is given in Table 5. Further averages include induced dipole moments if polarizabilites are present , various chain averages if chains are present , and the radius of gyration of hierarchical structures if present. In the same manner as for control quantities, the averages of main quantities are written after each macrostep and grand averages are written after the simulation.
Thermodynamic integration is a method to evaluate the free energy difference between two different states. Table 6 provides a list of the distributions functions available. Their grand average and precision can be i visualized, ii written to the output file, and iii listed in a list file in a form more convenient for plotting. As mentioned in the MOLSIM Main Structure section, a number of particle properties can be written to and read from various dump files, one file for each property. The list of properties available includes particle positions and orientation, particle linear and angular velocity, forces and torques acting on particles, and particle induced dipole moments.
The dumped data can be used to perform analyses after the generation of configurations , see the Top organization and Working protocols sections.
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All dumped quantities are written in full representation and bitwise identical results are obtained from analyses made on the fly and after the generation of the positions etc, see Figure 1. However, sometimes a division of the particles in a different manner is desired. MOLSIM offers the possibility to divide particles of a given type into two or several groups based on various criteria. A list of static properties available is given in Table 7.
To invoke any of them, a master flag switch has to be enabled, and thereafter another flag for the specific property also needs to be enabled. Finally, more specific input information for that property can be provided. Most of the analyses use the group division described in Group Division section, enabling a detailed control of the selected particle investigated.