Simple Dynamics Lesson, Input File

When you execute most of the commands in the Discover_3 module, you are actually building up a command input file, which is written to disk when the D_Run/Run command is executed. The command input file consists of a BTCL script that controls the Discover run.

This example file contains links to the complete descriptions of the BTCL commands. The BTCL language. Added comments that were not part of the original file are in italics.

Default values that are not specified in the command input file are shown in the output file.

#BIOSYM btcl 3
#
#  Input File For Discover Generated By Insight Version 2.95.0
#  Date:	   Tue Nov  8 13:27:20 1994
#  Host Name: iris90  	Host Type: iris
#
begin
#
#

The first dynamics command controls the equilibration stage:

#
dynamics \
  time = 1000.0 timestep = 1.0 \
  initial_temperature = 298.0 +boltzmann \
  ensemble = nvt temperature_control_method = velocity_scaling \
  integration_method = Velocity_verlet \
  temperature = 298.0 temperature_window = 10 \
  deviation = 5000 \
  execute +before frequency = 10 last_step = 0 +after \
    command = {print output \
    +instant \
    +average \
    +batch_average \
    batch_size = 10 \
    +total_energy \
    +kinetic_energy \
    +potential_energy \
    +temperature}
#
writeFile coordinate filename = .cor 
#

The second dynamics command controls the data-collection stage:

dynamics \
  time = 1000.0 timestep = 1.0 -boltzmann \
  ensemble = nvt temperature_control_method = velocity_scaling \
  integration_method = Velocity_verlet \
  temperature = 298.0 temperature_window = 10 \
  deviation = 5000 \
  execute +before frequency = 10 last_step = 0 +after \
    command = {print output \
    +instant \
    +average \
    +batch_average \
    batch_size = 10 \
    +total_energy \
    +kinetic_energy \
    +potential_energy \
    +temperature} \

A table file will be printed, for use in graphing the averages:

  execute +before frequency = 10 last_step = 0 +after \
    command = {print table \
    +instant \
    +average \
    +batch_average \
    +batch_sd \
    batch_size = 10 \
    +total_energy \
    +kinetic_energy \
    +potential_energy \
    +temperature} \

An archive file will be printed, for use in animating the molecule:

  execute +before frequency = 10 last_step = 0 +after \
    command = {print archive +coordinates}
#
writeFile coordinate filename = .cor

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Simple Dynamics Lesson, Introduction Simple Dynamics Lesson, Lesson