CHARMM c28a3 sbound.doc

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           Method and implementation of deformable boundary forces

        The use of deformable boundary forces is in studying small
localized regions of solvent, say around an active site.  The boundary
forces are applied to the atoms in the solvent and serve to contain
the reaction zone.

        Generally the boundary forces are computed from the deformable
boundary method of C. L. Brooks III and M. Karplus, J. Chem. Phys., 79,
6312(1983).  Following generation one must;

    i) Generate the corresponding boundary potential

   ii) Read the tabulated boundary potential into CHARMM

  iii) Set-up the mapping CHARMM uses to connect table entries with
       boundary constrained atoms

Steps ii) and iii) ** 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.

        The syntax for generating the potential and reading and setting up
the table structure is given in the following mode.

* Menu:

* Syntax::                             Syntax for all the SBOUnd commands
* Files: (support.doc)Boundary. Deformable boundary potential files

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          > SBOUnd POTEntial INPUt <integer> OUTPut <integer>

  Integrates forces to get potential and generates cubic spline
  approximation of the potential.

          > SBOUnd SET XREF <real> YREF <real> ZREF <real>
                   ASSIgn <table number> <selection-syntax>

  Solvent boundary routine to set boundary geometry
  and specify the atoms referring to the tables.  Note the
  assign must be repeated for each table entry.

           > SBOUnd READ UNIT <integer>

  This routine reads in the boundary potential splines
  for the boundary constraints.

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Information and HTML Formatting Courtesy of:

NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute