The ECHECK 1000000000 value is insane; anything over 500 is usually a bad idea. Large energy changes typically indicate a problem with the model building that needs to be fixed, not suppressed.

DO NOT use TIMESTEP greater than 0.002 for atomistic simulations; our group uses and recommends 0.001 for most work. You should only increase NSTEP to get a longer simulation time for a given run, or use multiple runs with DYNA RESTART. See dynamc.doc

The above scripts indicate a method for which can be used to run much longer simulations using the RESTART capability of CHARMM, and some shell scripts to partially automate file numbering, failure checks, and continuation.

Rick Venable
computational chemist