NB! BEGIN, SKIP and STOP have to be specified to allow proper
memory allocation! The TRAJ QUERY command can retrieve these values
The trajectory(ies) are read into memory before calculations begin;
Memory usage may be reduced by decreasing the number of selected atoms,
and by reducing the number coordinate sets (frames) used - increase SKIP
The error message, which is from RMSDyn, is simply not very informative, a lot like the documentation for this command. However, the above implies you must include BEGIN, SKIP and STOP as part of the command.