chrgall.

#!/bin/bash -l
#==========================================================================================
# chrgall.   ### This script takes the parameters that come from lchrgall. to calculate ###
#            ### the charge files for the different simulation configurations that      ###
#            ### exist. A more capable method would require a script that can determine ###
#            ### the parameters from the topol.top file, but which pore channel to      ###
#            ### examine (0 or 1) will remain a manual choice, possibly always since    ###
#            ### the computational cost is so high for even 1 pore. This more capable   ###
#            ### method has not been developed yet                                      ###
# parameters
# $1         number of vertical bins
#   options: typically 50 or 100
# $2         awk routine to execute
#   options: 3dchrg4[AHNPWSCRTYL].awk
# $3         atom charge file for this version of simulation topology
#   options: whatever you have named your charge file
# $4         output file name
# $5         pore channel number to process
#   options: 0 or 1
# $6         number of alpha bath ions of each species
#   explain: if alpha bath has 11 +tive and 11 -tive ions, (always neutral) enter 11
# $7         number of beta bath ions of each species
#__________________________________________________________________________________________

Chr1=${1:-'50'}
Chr2=${2:-'3dchrg4A.awk'}
Chr3=${3:-'chrgs2.xvg'}
Chr4=${4:-'test.xvg'}
Chr5=${5:-'0'}
Chr6=${6:-'0'}
Chr7=${7:-'11'}
Chr8=${8:-'11'}

s ../jobs/${Chr2} ${Chr1} ${Chr3} ${Chr4} ${Chr5} ${Chr6} ${Chr7} ${Chr8}