In most cases, use of 0.002 ps is tolerable (but not ideal) if one constrains the bonds to hydrogens via e.g.

SHAKE BONH PARAM

This removes the high frequency C-H, N-H, and O-H vibrations (think of an IR spectrum), and provides some rationale for the larger 0.002 ps timestep. However, we've observed differences in calculated properties between simulations run at 0.001 and 0.002 ps, so we mainly use the smaller 0.001 ps value.


Rick Venable
computational chemist