The Molecular Dynamics class (Motors) is a subclass of the Molecular Mechanics (MolMech) class. The Motors class is defined in the MolDynam module in Yup.Models. The import statement would be some variant of: from Yup.Methods.MolDynam import Motors. Data Attributes Data attribute names are case-sensitive. Two attributes (Temperature and ThermMethod) are read-only. This class will malfunction if these attributes are created in an assignment statement. To recover, delete the attributes that have been created. Read-only attributes must be set not by assignment but by calling the appropriate methods. In addition to these data attributes this class also inherits the attributes from the MolMech class: this means you have another set of attributes that you can query or set. Attribute Description StepSize The step size to be used in the integration of the equations of motion. The preset value is 0.001 and the unit is picosecond. ThermalizationInterval The number of steps between adjustment of the velocities. The velocities are adjusted to the current target temperature using a thermalization method. The preset value is 0, which means no adjustment. CollisionFrequency The default value is 0.0 ps-1. Langevin dynamics will be carried out if this is greater than 0.0. Otherwise, Newtonian dynamics. CouplingConstant The is the ratio of the step size over the coupling time constant (of the Berendsen heat bath) and is therefore dimensionless. The preset value is 0.01. Temperature This is read-only. Returns the current temperature [K]. To force the model to a specific temperature, use the set_Temperature() method. ThermMethod This is read-only. Returns the name of the current thermalization method. To set a thermalization method use the set_ThermMethod() method. VelocityArchive Name of archive into which the Velocities will be written at intervals defined in the MolMech.ArchiveInterval attribute. The default value is a blank string which means that this archive is not created regardless of the value of the ArchiveInterval attribute. Methods The Motors class defines the constructor function and three methods. The constructor function requires one argument, the model on which the molecular dynamics method is to be applied. This is a Model object that is constructed by a force field assembler. Constructor Number of Arguments Return Value Motors 1 The new Motors object Argument Purpose Preset Value a Model object the model that is to be subjected to the molecular mechanics calculation - The model object must be complete, i.e., the Map, Energy and Coordinates attributes must all be defined. The set_ThermMethod method selects the thermalization method that is to be used to adjust velocities. Method Argument Keyword Return Value set_ThermMethod "method" - Argument Type Preset Value method String - The method names are: 'NEW', 'SCALE' and 'BERENDSEN'. The default setting is 'NEW'. With the 'NEW' method, the velocities are generated from a Gaussian distribution so that the temperature of the model is at the target value. With the 'SCALE' method, the velocities are scaled so that the temperature of the model is at the target value. The 'BERENDSEN' method simulates a loosely coupled heat bath and the degree of coupling can be adjusted with the CouplingConstant attribute. The set_Temperature method adjusts the velocities to force the model to the specified temperature. Method Argument Keyword Return Value set_Temperature "T" - Argument Type Preset Value T Float - ranseed Integer 0 If the prevailing temperature is below 0.1K, the velocities are set to the specified value of T from the Gaussian distribution. If the model is at a higher temperature, the velocities are scaled to the specified value. The second argument can be used to cause the random number generator to be seeded with a non-default value. With the default argument value of 0, there is no change in the procedure described in the above paragraph. If ranseed has a positive value, that value is used to seed the random number generator. If ranseed is negative, then the current time (number of seconds since the beginning of system time) is used to seed the random number generator. The Verlet method carries out a molecular dynamics calculation using the Verlet method. Method Argument Keywords Return Value Verlet "numstep", "limit" - Argument Type Preset Value numstep Integer - target Float None limit None, a group AtomMap, or a list of two integers None Molecular dynamics can be restricted to a portion of a system. Please see the Targeted Simulation section of the Introduction to see how to set limit. Molecular dynamics is carried out over numstep integrations of the equations of motion. The time interval is therefore StepSize x numstep in units of picoseconds. The velocities are updated using the selected thermalization method every ThermalizationInterval steps. If target is None, the velocities are adjusted to the prevailing temperature. If target is a temperature in K, the velocities are adjusted every ThermalizationInterval steps to the target temperature that is on a linear trend between the starting temperature and the value of target. With the CollisionFrequency at the default value of 0.0 ps-1, regular Newtonian dynamics will be carried out. If set above 0.0, Langevin dynamics will be carried out. The Energies method provides a listing of components of the potential energy, the gradient norm, the kinetic energy, the total energy and the temperature. Method Argument Keywords Return Value Energies "option" - Argument Type Preset Value option Integer 0 In the default, the listing consists of a title line followed by a blank line (1), the labels (2), the energy values (3) and a blank line followed by a summary (4). Partial listings can be obtained by calling this method with the option argument set to any of the four numbers listed within parentheses. Example >>> from Yup.Models.TestTube.FFA import makecircle >>> from Yup.Methods.EnerMinim import Minimizers >>> from Yup.Methods.MolDynam import Motors >>> >>> M = makecircle( 100 ); O = Minimizers( M ); D = Motors( M ) >>> >>> D.set_ThermMethod( 'BERENDSEN' ) >>> D.ThermalizationInterval = 25 >>> minimize = O.SteepestDescent >>> dynamics = D.Verlet >>> >>> minimize( 1000 ); dynamics( 10000, 300.0 ); dynamics( 10000, 300.0 ); dynamics( 10000, 1.0 ); minimize( 1000 ) In this example, we start with the required imports: the makecircle() method from the TestTube force field assembler, the Minimizers class from the Energy Minimization module and the Motors class from the MolDynam module. The makecircle() method assembles the force field for a circular chain of beads, and the example asks for a chain of 100 beads and the Model that is returned is saved in the variable M. M is then passed to the Minimizers() constructor function and the object that is returned is then saved in the variable O. A Motors object is also constructed and saved in the variable D. The thermalization method is set to 'BERENDSEN' using the set_ThermMethod() method and the thermalization interval is set to 25. The steepest descent method is selected from the EnerMinim class and saved to the variable minimize. Similarly, the Verlet method is selected from the Motors object and assigned to the variable dynamics. The calculation consists of 1000 steps of energy minimization at the start and again at the end of the procedure. In between, molecular dynamics simulations are carried out in three blocks of 10000 steps each. In the first block the temperature is raised from the starting value which is 0K to 300K. In the next block the temperature is maintained at 300K. In the final block the temperature target is lowered to 1K. Introduction Molecular Mechanics Energy Minimization Molecular Dynamics Monte Carlo