Why is the timestep incorrect in DCD files?
I assume you are using X-PLOR to read the trajectories. A couple of years ago, after X-PLOR development stopped, the NAMD DCD format was adjusted slightly to conform to the CHARMM specification. The difference between the two is that while X-PLOR used a double for the timestep, CHARMM uses the same space for a float followed by an int. That int is important because it indicates if the file contains data about the periodic cell, a recent addition. It was previously ignored so CHARMM and X-PLOR could exchange DCD files with only a bad timestep, but now CHARMM rejects X-PLOR written files unless the timestep is zero. I would suggest trying to cope with the incorrect timestep. If you can’t the NAMD source distribution contains dumpdcd.c and loaddcd.c, which can be used to set the headers to whatever you want, and fixdcd.c, which can be modified to fix your problem (it currently changes X-PLOR to CHARMM).
