LIN : A New Algorithm to Simulate the Dynamics of Biomolecules by Combining
Implicit-Integration and Normal Mode Techniques
A central goal in molecular dynamics simulations is increasing the integration
time-step to allow the capturing of biomolecular motion on biochemically
interesting time frames. We previously made a step in that direction by
developing the Langevin/implicit-Euler scheme. Here, we present a modified
Langevin/implicit-Euler formulation for molecular dynamics. The new method
still maintains the major advantage of the original scheme, namely, stability
over a wide range of time-steps. However it substantially reduces the damping
effect of the high-frequency modes inherent in the original implicit scheme.
The new formulation involves separation of the solution into two components,
one of which is solved exactly using normal mode techniques, the other
of which is solved by implicit numerical integration. In this
way, the high-frequency and fast varying components are well resolved in
the analytic solution component, while the remaining components of the
motion are obtained by a large time-step integration phase. Full
details of the new scheme are presented, accompanied by illustrative examples
for a simple pendulum system. An application to liquid butane demonstrated
stability of the simulations at time-steps up to 50 fs, still with activation
of the high frequency modes.
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