Exact and efficient calculation of derivatives of Lagrange multipliers for molecular dynamic simulations of biological molecules
Abstrak
In the simulation of biological molecules, it is customary to impose constraints on the fastest degrees of freedom to increase the time step. The evaluation of the involved constraint forces must be performed in an efficient manner, for otherwise it would be a bottleneck in the calculations; for this reason, linearly-scaling calculation methods have become widely used. If integrators of order higher than 2 (e.g. Gear predictor-corrector methods) are used to find the trajectories of atoms, the derivatives of the forces on atoms with respect to the time also need to be calculated, which includes the derivatives of constraint forces. In this letter we prove that such calculation can be analytically performed with linearly scaling numerical complexity (O(Nc), being Nc the number of constraints). This ensures the feasibility of constrained molecular dynamics calculations with high-order integrators.
Topik & Kata Kunci
Penulis (1)
Pablo García-Risueño
Akses Cepat
- Tahun Terbit
- 2019
- Bahasa
- en
- Sumber Database
- arXiv
- Akses
- Open Access ✓