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• W1520064037 abstract "Molecular dynamics simulations have provided invaluable insight into the properties of biomolecular and other systems. Unfortunately, biomolecular simulations are often computationally demanding due to the large number of particles that involve complex and long-range interactions. With the Ewald summation technique, the long-range pairwise Coulomb interactions, the dominant computational task, can be efficiently and accurately evaluated. Despite this progress, modeling most biomolecular simulations that require very long time scales is still a grand challenge that few researchers can afford to take. However, a new algorithm, the multiple time step (MTS) integration method, can dramatically reduce the computational cost. Nevertheless, the MTS methods can introduce errors and instabilities in certain circumstances. In this dissertation, we analyze the properties of a simple 1D linear system integration with the symplectic reference system propagator (r-RESPA) MTS method. A closed form expression for the time step dependent Hamiltonian which corresponds to r-RESPA integration of the model is derived. This allows us to present an analytical formula for the dependence of the integration accuracy on the short-range force cutoff. A detailed analysis of the force decompositions for the standard Ewald summation method is given. We test the analysis on a realistic system, a protein in water. Under Langevin dynamics with a weak friction coefficient to control temperature and with the SHAKE algorithm to freeze out high frequency vibrations, we show that the five femtosecond (fs) resonance barrier is postponed to approximately 20 fs. An iso-error curve in a system involving the short-range cutoff versus the multiple time step size agrees well with the analytical results. Using r-RESPA to treating long-range interactions results in a six times of increase in efficiency for the distance-based force decomposition with independent Ewald and short-range cutoffs." @default.
• W1520064037 created "2016-06-24" @default.
• W1520064037 creator A5020349055 @default.
• W1520064037 creator A5047165687 @default.
• W1520064037 date "2006-01-01" @default.
• W1520064037 modified "2023-09-26" @default.
• W1520064037 title "Analysis of multi-scale molecular dynamics algorithms for simulating biomolecules" @default.
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• W1520064037 hasPublicationYear "2006" @default.
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