16.2 Using the Analysis Facility

To call the analysis facility of CONGEN, one places ANALYSIS as the first and only word on a command line (it may be abbreviated to four characters). Prior to calling the analysis facility, the user must have taken the following steps: A PSF must have been read or constructed. A parameter set and complete coordinate set are required also. If hydrogen coordinates are missing from the coordinate set or if hydrogen bonds are to be analyzed, a HBONDS command must have specified before the ANALYSIS command (see Hydrogen Bonds). Likewise, if non-bonded interactions are to be analyzed, an NBONDS command must be invoked prior to analysis (see Non-bonded Interactions). If the total energy per atom is to be analyzed, then both NBONDS and HBONDS must be specified.

Although the analysis facility has a command interpreter which is different from that in the main program, commands are specified in free field format, as in the main part of CONGEN, see Run Control. To exit the analysis facility, use the END command, which is just the word, END, on a command line by itself.