A modified shake algorithm for maintaining rigid bonds in molecular dynamics simulations of large molecules (Q1263954)

The presented method gives from physical point of view an interpolation of constraint force and provides a basis for monitoring various aspects of bond stress in molecular dynamics simulations. The MSHAKE algorithm, which is applied by modifying the leapfrog algorithm to include forces of constraint, computes an initial estimate of constraint forces and iteratively corrects the constraint forces required to maintain the fixed distances. This is made by two mathematical steps: - calculation of an estimate using a finite-difference scheme, - calculation of corrections using iterative relaxation. Finally the calculation of multiple constraints from the standpoint of constraint force functions is described, especially in cases where the bond stress is important as position and velocity.