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Moloc: Molecular Modelling on UNIX Workstations: 19 Dynamics [dyn]

Dynamics [dyn]

Various dynamics facilities are available here. Dynamics can be run on all-atom and on Calf structures. Trajectory files generated by batch runs (.mac or .mcc files) can be viewed and analyzed.

In addition, graphs of energy versus one to three torsional angles can be produced.

Furthermore, a few facilities provide interfaces to other force field packages: GROMOS, XPLOR, and TNT.

Drive Dihedral Angles [drv]

Up to three torsional angles can be varied systematically to produce an energy map. Previously produced maps can be examined.

View Trajectories

Trajectories generated by dynamics batch-runs can be viewed here. Various options to simplify the display procedure are available.

Trajectory Evaluations [ctc]

Several quantities can be analyzed along a trajectory. First the quantities of interest must be specified (e.g. a distance) for which a analysis is required. In addition a set of time values can be set that influence the mode of evaluation. Upon choosing the type of analysis the user is asked to specify a trajectory file. After evaluation of each trajectory file the program asks for a continuation file. If no such must be read, the file requester must be left with the escape key. At this stage the program presents the results as graphs. Correlation function and power spectrum are displayed in two separate graphs.

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