Constrained molecular dynamics: Difference between revisions

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[[Category:Molecular Dynamics]][[Category:Theory]][[Category:Howto]]
[[Category:Molecular Dynamics]][[Category:Constrained molecular dynamics]][[Category:Theory]][[Category:Howto]]

Revision as of 12:06, 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:

  1. Perform a standard MD step (leap-frog algorithm):
  2. Use the new positions q(tt) to compute Lagrange multipliers for all constraints:
  3. Update the velocities and positions by adding a contribution due to restoring forces (proportional to λk):
  4. repeat steps 2-4 until either |σi(q)| are smaller than a predefined tolerance (determined by SHAKETOL), or the number of iterations exceeds SHAKEMAXITER.

References