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| == References == | | == References == |
Revision as of 14:54, 13 March 2019
Constrained molecular dynamics is performed using the SHAKE algorithm.[1].
In this algorithm, the Lagrangian for the system is extended as follows:
where the summation is over r geometric constraints, is the Lagrangian for the extended system, and λi is a Lagrange multiplier associated with a geometric constraint σi:
with ξi(q) being a geometric parameter and ξi is the value of ξi(q) fixed during the simulation.
In the SHAKE algorithm, the Lagrange multipliers λi are determined in the iterative procedure:
- Perform a standard MD step (leap-frog algorithm):
- Use the new positions q(t+Δt) to compute Lagrange multipliers for all constraints:
- Update the velocities and positions by adding a contribution due to restoring forces (proportional to λk):
- repeat steps 2-4 until either |σi(q)| are smaller than a predefined tolerance (determined by SHAKETOL), or the number of iterations exceeds SHAKEMAXITER.
Anderson thermostat
References