What to Read

This user manual starts with a semi-tutorial ``Getting Started'' (Chapter 2) followed by chapters which describe the organization and structure of the EGO program in more detail. Several appendices summarize other relevant information such as file formats, and the differences between EGO and X-PLOR program. Read Chapter 2 for a quick introduction on how to create an EGO dataset and run a simple simulation. (You might have to use the structure editing features of the X-PLOR program to create the needed PSF topology description files for your PDB files and molecule structures).

Chapter 4 describes the dynamics control parameter settings in more detail.

Chapters 5 and 6 describe the implementation of the program and the modified Verlet integration method used by EGO, respectively.