The lis-file ctl.lis contains important simulation parameters, which influence your molecular dynamics calculation and, hence, we call it the control file. In this chapter all parameters which can be set in that control file will be described in detail. Since the computation of the energy function in EGO is based largely on that described in the X-PLOR software package, this chapter will contain frequent cross-references to the X-PLOR User's Manual Version 2.1  for further clarifications.
The control file consists of three sections. The first section is made up from a list of lis-files, which give the full description of the model system, e.g., the position of each atom (coord_300K.lis) and bond parameters (bondpara.lis). The second section specifies all necessary simulation parameters, e.g., the number of integration steps to be performed. This section has a fixed format and no line must be deleted or inserted. The third section is optional and follows after the last line containing 'DEBUG'. This section is in a free format.
The conversion program xpl2lis sets up a control file ctl.lis which may be regarded as a template file. In this template file most of the parameters given in the second section are set to reasonable values; no third section is included in that template file. Make a copy of the template file and change the parameters in order to meet your intended simulation.