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NIH: National Institute of Diabetes and Digestive and Kidney Diseases NIH: National Institute of Diabetes and Digestive and Kidney Diseases

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Next: Syntax Up: Deformable Boundary Forces Previous: Deformable Boundary Forces


The Solvent Boundary Method

Generally the boundary forces are computed from the deformable boundary method of Brooks and Karplus (1983). Following generation one must

  • Generate the corresponding boundary potential
  • Read the tabulated boundary potential into XPLOR
  • Set-up the mapping XPLOR uses to connect table entries with boundary constrained atoms

The second and third steps ** MUST ** be done everytime the boundary forces are to be used. For example, during the initial stages of a dynamics simulation and at all subsequent restarts.



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