Improving efficiency of large time-scale molecular dynamics simulations ofhydrogen-rich systems

A systematic analysis is performed on the effectiveness of removing degrees of freedom from hydrogen atoms and/or increasing hydrogen masses to increa se the efficiency of molecular dynamics simulations of hydrogen-rich system s such as proteins in water. In proteins, high-frequency bond-angle vibrati ons involving hydrogen atoms limit the time step to 3 fs, which is already a factor of 1.5 beyond the commonly used time step of 2 fs. Removing these degrees of freedom from the system by constructing hydrogen atoms as dummy atoms, allows the time step to be increased to 7 fs, a factor of 3.5 compar ed with 2 fs. Additionally, a gain in simulation stability can be achieved by increasing the masses of hydrogen atoms with remaining degrees of freedo m from 1 to 4 u. Increasing hydrogen mass without removing the high-frequen cy degrees of freedom allows the time step to be increased only to 4 fs, a factor of two, compared with 2 fs. The net gain in efficiency of sampling c onfigurational space may be up to 15% lower than expected from the increase in time step due to the increase in viscosity and decrease in diffusion co nstant. In principle, introducing dummy atoms and increasing hydrogen mass do not influence thermodynamical properties of the system and dynamical pro perties are shown to be influenced only to a moderate degree. Comparing the maximum time step attainable with these methods (7 fs) to the time step of 2 fs that is routinely used in simulation, and taking into account the inc rease in viscosity and decrease in diffusion constant, we can say that a ne t gain in simulation efficiency of a factor of 3 to 3.5 can be achieved. (C ) 1999 John Wiley & Sons, Inc.