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A fast mollified impulse method for biomolecular atomistic simulations. (English) Zbl 1375.92022
Summary: Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work, we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice-ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as \(10\;\text{fs}\) while keeping the energy drift less than 1% on a \(50\;\text{ps}\) simulation.
92C40 Biochemistry, molecular biology
74S30 Other numerical methods in solid mechanics (MSC2010)
74L15 Biomechanical solid mechanics
Full Text: DOI
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