NAMD configuration file

Besides these input and output files, NAMD also uses a file referred to as the configuration file. This file specifies what dynamics options and values that NAMD should use, such as the number of timesteps to perform, initial temperature, etc. The options and values in this file control how the system will be simulated.

A NAMD configuration file contains a set of options and values. The options and values specified determine the exact behavior of NAMD, what features are active or inactive, how long the simulation should continue, etc. Section 2.2.1 describes how options are specified within a NAMD configuration file. Section 2.2.2 lists the parameters which are required to run a basic simulation. Section 6 describes the relation between specific NAMD and X-PLOR dynamics options. Several sample NAMD configuration files are shown in section 7.

Configuration parameter syntax

Each line in the configuration files consists of a keyword identifying the option being specified, and a value which is a parameter to be used for this option. The keyword and value can be separated by only white space:

keyword            value

or the keyword and value can be separated by an equal sign and white space:

keyword      =     value

Blank lines in the configuration file are ignored. Comments are prefaced by a # and may appear on the end of a line with actual values:

keyword            value          #  This is a comment

or may be at the beginning of a line:

#  This entire line is a comment . . .

Some keywords require several lines of data. These are generally implemented to either allow the data to be read from a file:

keyword            filename

or to be included inline using Tcl-style braces:

keyword {
  lots of data
}

The specification of the keywords is case insensitive so that any combination of upper and lower case letters will have the same meaning. Hence, DCDfile and dcdfile are equivalent. The capitalization in the values, however, may be important. Some values indicate file names, in which capitalization is critical. Other values such as on or off are case insensitive.

Required NAMD configuration parameters

The following parameters are required for every NAMD simulation:

• numsteps (page ),

• coordinates (page ),

• structure (page ),

• parameters (page ),

• exclude (page ),

• outputname (page ),

• one of the following three:
  • temperature (page ),

  • velocities (page ),

  • binvelocities (page ).

These required parameters specify the most basic properties of the simulation. In addition, it is highly recommended that pairlistdist be specified with a value at least one greater than cutoff.