begin

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Purpose

The begin command is placed at the start of the main commands section of the command input file. It reads in the molecular data files (.car and .mdf) and the forcefield.

Syntax

begin ?keyword = value?...



Keyword         Values   Default               Meaning


coord*inate     string   run_name.car     Name of coordinate data file. If none
   or car                                 given, defaults to run_name.car.

topol*ogy       string   run_name.mdf     Name of molecular data file that
   or mdf                                 defines connections, etc. If none 
                                          given, defaults to run_name.mdf.

forcef*ield     string   $FORCEFIELD      Name of forcefield file. If none 
                                          given, defaults to value of the 
                                          $FORCEFIELD environment variable.

Description

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The begin command is the first Discover command to be executed in the input file. It reads in the molecular system and the forcefield parameters. It does not set up the energy expression or the nonbond list. This is done the first time an energy calculation is requested (e.g., by a minimize command).

The typical use of the begin command does not specify any filenames. The molecular data are then picked up from the .car and .mdf files corresponding to the current run, and the forcefield is specified by the environmental variable $FORCEFIELD (same as for the Insight program).

Example 1

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begin

This example of the begin command uses the default molecular data and forcefield file assignments.

Example 2

begin forcefield = cvff

This example of the begin command uses the default molecular data files but explicitly reads the CVFF forcefield.

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