#!/bin/bash
## Script will extract the base-pair parameters
## and genereta a plot of each individual base-pair
## using the nastruct command of CPPTRAJ and GNUPLOT
cpptraj='/uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber/bin/cpptraj'

cd ~/gaac/anton/analysis/base-opening


$cpptraj ../../GAAC-ions.topo <<EOF
trajin ../../GAAC-strip.netcdf 1 999999999 1
distance d1 @19 @1130 out anton1.dat
distance d2 @53 @1096 out anton2.dat
distance d3 @83 @1067 out anton3.dat
distance d4 @115 @1031 out anton4.dat

distance d5 @464 @684 out anton5.dat
distance d6 @496 @650 out anton6.dat
distance d7 @525 @621 out anton7.dat
distance d8 @559 @587 out anton8.dat


EOF