1. Molecular dynamics simulation method combining reversible multi-time scale integration and fast multipole method
The fast multipole method (FMM) is a fast algorithm for calculating long-range electrostatic interactions between particles, while reversible multiscale integration (r-RESPA) is an algorithm that integrates the equations of motion separately for different time scales of the system. The r-RESPA/FMM method allows the use of faster time steps under the condition of similar accuracy as the velocity verlet integration algorithm. in an effort to improve the efficiency of noncubic or nonuniform systems. By using r-RESPA/ FMM, MD simulations can be performed for very large biomolecules, since the memory and CPU time requirements are now almost O (N) instead of O (N2).
Coulomb potential expansion multipoles: Reversible multi-time scale integration
2. Hydrophobic-assisted copy exchange: an efficient algorithm for protein folding in explicit solvents.
Indirectly increase hydrophobicity inside the protein by only attenuating the interaction between the protein and the aqueous solvent balancing the exchange of copies of different λ by the Metropolis method
Faster protein folding could be realized with fewer copies compared with traditional copy exchange methods
3. Copy exchange in solute annealing
The ratio between the growth of the number of copies required by the conventional copy exchange method and the growth of the degrees of freedom f in the system is O(f1/2), which makes it difficult to relate the conventional copy exchange method to computations of large systems. In contrast, copy exchange in solute annealing requires a growth of the number of copies with respect to the growth of the degree of freedom f of the system of O(fp1/2), where fp is the degree of freedom of the selected solute in the system, which is more efficient for sampling large systems.
