Add some trajectory analysis scripts

trajectory_analysis/2-ndx.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+out_dir="$(basename ${0})"
+out_dir="${out_dir%%.*}"
+
+# create array of system names
+
+ARR1=()
+for i in 1-concat/individual/*/*/ ; do
+    ARR1+=($(basename ${i}))
+done
+
+# make directory and create ndx files
+
+mkdir -p "${out_dir}"
+
+while read system; do
+    ARR2=("${out_dir}/individual/*/${system}/${system}-*.pdb")
+    ARR3=("${out_dir}/individual/*/${system}/${system}.ndx")
+    gmx make_ndx -f ${ARR2[1]} -n ${ARR3[1]} -o "${out_dir}/${system}.ndx"
+done < <(echo ${ARR1[@]} | tr " " "\n" | sort -u)