NAMD was developed to be compatible with existing molecular dynamics packages, especially the packages X-PLOR [7] and CHARMM [6]. To achieve this compatibility, the set of input files which NAMD uses to define a molecular system are identical to the input files used by X-PLOR and CHARMM. Thus it is trivial to move an existing simulation from X-PLOR or CHARMM to NAMD. A description of these molecular system definition files is given in Section 3.1.
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. Descriptions of the output files formats are also given in Section 3.1.