Looks like it is possible to get up to 10 ns/day for a system with 260,000 atoms. Here are the parameters (that I borrowed from charmm-gui output): nstep = 50000 # Number of steps to run dt = 0.002 # Time-step (ps) nstout = 1000 # Writing output frequency (steps) nstdcd = 5000 # Writing coordinates ...