Hello,
Could it be an occurrence of the flying ice cube effect ? Are you using the Berendsen thermostat? If so, you may want to consider another thermostat, or/and try to cancel any center of mass motion that may occur.
Simon
You can still quote the relevant sections of your input files and read the forum guidelines. Also, knowing which temperature and units were used would be useful.
A time step of 1fs for flexible water is bound to give wrong results, even 0.5fs is “ambitious”. The virbrational modes of the OH bonds are too fast to be accurately represented by such larger timesteps.