The first part of CONGEN's output after a dynamics command lists all of the options that apply to that part of the run. Then, any information about velocity assignments (temperature changes) follows. Any time the velocities are changed in an anisotropic way, the motion of and about the center of mass will be stopped. This results in a printout both before and after this operation of the `DETAILS ABOUT CENTRE OF MASS'. Its position and velocity are output followed by the components of the angular momentum. The last line gives the translation kinetic energy of the system, and thus one should expect a drop in the total energy and temperature of the system afterwards.
Non-bonded interaction and hydrogen bond updates will appear intermittently and are cleared labeled.
Every NPRINT steps, the total energy and various contributions will be printed. This output is preceded by a title which gives the correspondence of numbers to energy names. After IPRFRQ steps will appear the averages and RMS fluctuations. After the second such printout of averages and RMS fluctuations, the averages and RMS fluctuations for the run up to the last turning of the molecule will be given. This gives you longer range statistics. Such a calculation will not be done if IPRFRQ equals NTRFRQ. The ratio of total energy to kinetic energy fluctuations is an excellent measure of the accuracy of the run.
After the averages are printed, a least squares fit of the total energy against the step number will be made to look for drift in the energy. Two such values are printed, one for the last IPRFRQ steps, and one to the previous turn. Next, the initial energy for the statistics, both short range and long, are printed. Finally, the correlation coefficient of the energy versus step is given for both ranges. A value close to zero indicates no systematic drift; a magnitude near 1 means you have a real problem with the dynamics.
This process of printout continues until the end of the run is reached. Just before the last energy is printed will appear a message about the writing of coordinates and velocities to their respective files.