initial commit

create_emin.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+get_ini_value() {
+    local file=$1
+    local section=$2
+    local key=$3
+
+    awk -F '=' -v section="$section" -v key="$key" '
+    $0 ~ "\\[" section "\\]" { in_section = 1; next }
+    in_section && $1 ~ "^" key"[[:space:]]*$" {
+        gsub(/[[:space:]]+/, "", $2)
+        print $2
+        exit
+    }
+    $0 ~ /^\[/ { in_section = 0 }
+    ' "$file"
+}
+
+
+simdir="00_em"
+
+
+rm -r "$simdir" 2>/dev/null
+mkdir "$simdir"
+
+cp topology.top "$simdir/"
+../replace_params.sh params.ini topology.top --output "$simdir/topology.top"
+../replace_params.sh params_emin.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
+../replace_params.sh params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
+cp ../run.sh "$simdir/"
+cp "../gro_$(get_ini_value params.ini params model).gro" "$simdir/gro_start.gro"
+
+echo "emstep                   = 0.001" >> $simdir/mdp_parameters.mdp
+
+