Simple Dynamics Lesson, Instructions

Note--You must have completed the lesson on Minimizing a Molecule before starting this lesson.

  1. Setting up the dynamics calculation by selecting the system

    Select the Setup/System command and set the Disco Object Name to CYCLO0. Select Execute.

    This action informs the Discover system that you want to work on the CYCLO0 molecule.

  2. Setting up the equilibration stage of dynamics

    (This is equivalent to ``initializing dynamics'' in versions 2.9.x of the Discover program.)

    Select the Calculate/Dynamics command and make sure the following parameters are set:
    Activations - Add
    Stage Name - 2 dynamics
    More - off
    Run Time fs - 1000.0
    Velocity - Create
    Non PBC Ensemble - NVT
    Temperature K - 298.0
    Select Execute.

    What you are doing is setting up the command input file--the Discover program does not actually run until the D_Run/Run command is executed.

  3. Setting up the data-collection stage of dynamics

    (This is equivalent to ``resuming dynamics'' in versions 2.9.x of the Discover program.)

    Still in the Calculate/Dynamics parameter block, make sure these parameters are now set:
    Stage Name - 3 dynamics
    Velocity - Current
    Leave the other parameters at their current default values and select Execute.

    Note that Velocity becomes Current instead of Create, as it was for the previous stage.

    You may select Cancel to put away the Dynamics parameter block.

  4. Specifying the output for both dynamics stages

    Select the Analyze/Output command. Set the Stage Name to 2 dynamics, by choosing it from the value-aid.

    Notice that the default values for parameters correspond to those used in the last-specified stage, i.e., the minimization of the previous lesson.

    Assure that the other parameters are as follows:
    Delete_File_Type - off
    File Type - Output
    Discover File Name - default
    Before - on
    During - on
    Write Freq Steps - 10
    First Step No - 1
    Last Step No - end
    After - on
    Instant - on
    Running - on
    Batch - on
    Batch Freq Steps - 10
    Energy_Output - on
    Total_E - on
    Kinetic_E - on
    Potential_E - on
    Temperature_Output - on
    all other parameters - off
    Select Execute.

    This action inserts commands in the command input file that specify what kinds of output you want and when you want it during the equilibration stage of the dynamics run.

    Now select 3 dynamics as the Stage Name and select Execute.

    This action inserts commands in the command input file that specify what kinds of output you want in the output file and when you want it during the data collection stage of the dynamics run.

    Leave Stage Name as 3 dynamics and change File Type to Table. Select Execute.

    You have specified the output that is to go to a table file. The table file will be used to graph the running and batch averages of the total energy, potential energy, and temperature.

    Change File Type to Archive. Select Execute.

    You have specified the output that is to go to an archive file. The archive file will be used to animate the trajectory of the dynamics run.

  5. Running the dynamics simulation

    Select the D_Run/Run command and assure that the Run_Name is cyclo01. Select Execute to start the calculation.

    At any time after this step, you may compare your input file with an annotated copy of the input file, by going to a different shell window (i.e., not the one from which you started the Insight program) and using the UNIX cd command to go to your tutorial directory, then the more command to list the cyclo00.inp file.

    The run takes about two and a half minutes on an SGI Indigo2. You may check whether it has completed by executing the Background_Job/Completion_Status command.

  6. Viewing the output

    Wait until a notifier window appears, informing you that the run is complete. Select Continue to put away this window.

    To examine the output file, select the Session/Unix command and select Execute. Wait until a shell window and a UNIX prompt appear, then list the output file by entering the following command at the UNIX prompt (represented by >): 

    > more cyclo01.out
    You may compare your output file with an annotated copy of the output file.

    You should examine the Dynamics Summary sections that follow each dynamics command (summary after equilibrium, summary after data collection). Check the temperature and energies.

    After viewing the output file, return to the Insight environment by typing exit at the UNIX prompt and then selecting the Textport button.

  7. Animating the dynamics trajectory

    Go to the Module pulldown (that is, click the Biosym logo) and select Analysis.

    The Analysis module's pulldowns appear on the lower menu bar.

    Select the Trajectory/Get command.

    Choose cyclo01.arc as the Trajectory File, click the molecule to fill in Trajectory Object, and select Execute.

    You may select Cancel to put away the parameter block.

    Select the Trajectory/Animate command and select Execute.

    The molecule is animated according to the dynamics trajectory. The total energy for each animation frame is also indicated.

    Select the Trajectory/Unanimate command. Select Execute to stop the animation.

  8. Plotting the running and batch averages of the total energy, potential energy, and temperatures

    Select the Graph/Get command. When the parameter block appears, set the following parameter values:
    File Name - cyclo01.tbl
    X_Function - Time
    Y_Function - Total energy1
    Select Execute.

    A graph of the running average of the total energy vs. time appears. (You may have to cancel the parameter block to see your graph, which will be similar to, but not identical to, the illustration, because of the random nature of dynamics simulations.)

    Repeat this procedure, except choose Total energy2 as the Y_Function. Select Execute.

    A graph of the batch average of the total energy vs. time appears.

    Repeat the procedure for the potential energy and the temperature.

    You end up with a total of six graphs in the display area.

  9. Cleaning up the display area

    Select the Object/Delete command from the upper menu bar. Enter GRAPH* as the Object Name and select Execute. Allow the molecule to remain in the display area.

  10. Proceeding to the next lesson

    Do not quit the Insight program, but proceed to the lesson on Restarting a Dynamics Calculation or to its introduction.

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