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Syntax

SBOUnd
SBOUnd $<$sbound-statement$>$ END is invoked from the main level of X-PLOR.
$<$sbound-statement$>$:==
SET
SBOUnd $<$sbound-set-statement$>$ END * set up tables *
POTEntial
<sbound-potential-statement>
REFLect
<sbound-reflect-statement>
RESEt
reset parameters and origin
$<$sbound-set-statement$>$:==
ORIGin=$<$table number$>$ $<$vector$>$
specify origin for solvent boundary
AXIS $<$table number$>$ $<$vector$>$
specify direction of cylinder axis
ASSIgn $<$table number$>$ $<$selection-syntax$>$
assigns selected atoms to specified table
ATTAch $<$table number$>$ $<$attach statement$>$
attach solvent boundary to selected atoms
$<$attach-statement$>$:==
SELE=$<$selection-syntax$>$
RESEt
turn attach off, origin is used
SBETa $<$table number$>$ $<$real$>$
specify the boundary coupling sensitivity to the atoms to which it is attached 0=no sensitivity (attached to ORIGin) 1=instantaneous sensitivity (follows center of mass of selected atoms
MATRix ROWs=$<$integer$>$ COLUmns=$<$integer$>$
read table. Starting on the line following this statement the matrix is specified matrix(ROWs,COLUmns)
$<$sbound-potential-statement$>$:==
OUTPut=$<$filename$>$
has to be specified before MATRix
MATRix ROWS=$<$integer$>$ COLUmns=$<$integer$>$ $<$matrix-elements$>$

generates potential table (cubic splines) from force table by trapezoidal rule integration.

$<$sbound-reflect-statement$>$:==
reflects periodic box (26 images)
LBOX=$<$real$>$
ORIGin=$<$vector$>$
CUT=$<$real$>$
OUTPut=$<$filename$>$
new coordinates are written to file

Remark: Tables should be equidistant cubic splines listed as a matrix with 5 columns: radius, potential (Y), 1.-coef., 2.-coef, 3.-coef. The definition of the spline coefficients is: E = ( ( C(J,3)*D+C(J,2) )*D+C(J,1) )*D + Y(J)

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Xplor-NIH 2025-03-21