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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.
Xplor-NIH 2024-09-13