Molecular Input and Output File Formats

NAMD was developed to be compatible with existing molecular dynamics packages, especially the packages X-PLOR [6] and CHARMm [5]. To achieve this compatibility, the set of input files which NAMD uses to describe a molecular system are identical to the input files used by X-PLOR. These input files are very similar to those used by CHARMm. Thus it is trivial to move an existing simulation from X-PLOR to NAMD and requires minimal effort to convert a simulation from CHARMm to NAMD. In addition, the output file formats used by NAMD were chosen to be compatible with X-PLOR and CHARMm. In this way the output from NAMD can be analyzed using X-PLOR, CHARMm, or a variety of the other tools that have been developed for the existing output file formats.

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. The format and options used in this configuration file are described in Section 4.