Increasing the time step in molecular dynamics

✍ Scribed by Anna M. Nyberg; Tamar Schlick

• Book ID: 103034631
• Publisher: Elsevier Science
• Year: 1992
• Tongue: English
• Weight: 733 KB
• Volume: 198
• Category: Article
• ISSN: 0009-2614
• DOI: 10.1016/0009-2614(92)85028-9

✦ Synopsis

We examine how the two properties ofthe Langevinlimplicit-Euler scheme for molecular dynamics (MD) -stability over large time steps and damping of high-frequency vibrations greater than some cutoff frequency w, -affect the dynamics of a liquid butane model. For time steps At< 20 fs with a "natural" cutoff w,= ksT/h (k, and fi are Boltzmann's and Planck's constants, T= temperature), the associated kinetic energy is greater than 85% of its value at At= 1 fs, where the connection to a heat bath is weak and the generated trajectories by our scheme and conventional MD are similar. At larger At the connection to the heat bath is much stronger, and for At> 20 fs the intrinsic numerical damping of the scheme sets in. The comparison of bond-length and dihedral-angle distributions at three different time steps reveals a small, broadening trend at larger At. The differences in a dynamic property, the velocity autocorrelation function, are however much larger. There is a drastic difference for 2 and 20 fs, and for At> 40 fs most of the motion between time steps is damped and more random. Thus, while the Langevin equation per se gives a Boltzmann distribution, the expected configurational sampling can be obtained as long as the numerical damping does not disturb the balance between the random and damping terms. Consequently, for studying certain dynamic functions time steps in the same range as in conventional MD are needed, but for static properties larger time steps can be used.