Every time iAPBS module is executed it creates and writes to an auxiliary file named io.mc. This file can grow quite big when iAPBS is executed many times in succession, for example during minimization and molecular dynamics in implicit solvent. To disable writing to this file set MCSH_HOME environment variable to /dev/null before using CHARMM with iAPBS module. For example if using bash shell use this before running your calculation:
export MCSH_HOME=/dev/null |