New approaches for molecular dynamics simulations with nonholonomic constraints Original Research Article

Three new algorithms are described for imposing nonholonomic constraints in molecular dynamics (MD) simulations, with any additional holonomic constraints. These approaches address the drawbacks of the commonly used Gaussian approach, which requires analytical expressions of the constraint forces and thus can handle only small numbers of constraints, and which suffers from numerical drift in the constraints, necessitating the use of a constraint correction scheme. Of the three approaches described, the optimal one is a generalized SHAKE scheme, GSHAKE. Numerical results are given showing the advantages of GSHAKE over the Gaussian approach. In addition, GSHAKE is more advantageous than velocity scaling, for fixing the temperature during the equilibration phase of constant energy MD simulations.