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