diff --git a/polyamorphism_optimization/annealing.py b/polyamorphism_optimization/annealing.py
new file mode 100644
index 0000000..2c70d7e
--- /dev/null
+++ b/polyamorphism_optimization/annealing.py
@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+import shutil
+from pathlib import Path
+from generate_annealing import generate_annealing
+from replace_params import replace_params
+
+
+def main(root_dir: Path):
+    simdir = root_dir / "01_an1"
+
+    if simdir.exists():
+        shutil.rmtree(simdir)
+    simdir.mkdir()
+
+    # Copy topology and replace parameters
+    shutil.copy(root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params.ini", root_dir / "topology.top", simdir / "topology.top")
+    replace_params(root_dir / "params_an1.ini", root_dir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+    replace_params(root_dir / "params.ini", simdir / "mdp_parameters.mdp", simdir / "mdp_parameters.mdp")
+
+    # Copy run.sh
+    shutil.copy(root_dir / "run.sh", simdir / "run.sh")
+
+    # Generate annealing section
+    annealing = generate_annealing(d=50, l=50, u=1000, s=50, e=2000)
+    # -d 20 -l 750 -u 2100 -s 50 -e 10000 -c
+    with (simdir / "mdp_parameters.mdp").open("a") as f:
+        f.write("\n")
+        f.write(annealing)
+
+    print(f"Annealing directory {simdir} created and filled.")
+
+
+if __name__ == "__main__":
+    import sys
+    if len(sys.argv) != 2:
+        print(f"Usage: {sys.argv[0]} ROOT_DIRECTORY")
+        sys.exit(1)
+    main(Path(sys.argv[1]))
+
diff --git a/polyamorphism_optimization/create_annealing1.sh b/polyamorphism_optimization/create_annealing1.sh
deleted file mode 100755
index bca9576..0000000
--- a/polyamorphism_optimization/create_annealing1.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/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 }
-    ' "$file"
-}
-
-simdir="01_an1"
-
-
-rm -r "$simdir" 2>/dev/null
-mkdir "$simdir"
-
-cp topology.top "$simdir/"
-"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
-"$(dirname $0)/replace_params.sh" params_an1.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
-"$(dirname $0)/replace_params.sh" params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
-cp "$(dirname $0)/run.sh" "$simdir/"
-cp "00_em/out/out.gro" "$simdir/gro_start.gro"
-
-
-annealing=$($(dirname $0)/generate_annealing.py -d 50 -l 50 -u 1000 -s 50 -e 2000)
-
-#annealing=$($(dirname $0)/generate_annealing.py -d 30 -l 400 -u 950 -s 50 -e 2000)
-
-echo "" >> "$simdir/mdp_parameters.mdp"
-echo "$annealing" >> "$simdir/mdp_parameters.mdp"
-
-
diff --git a/polyamorphism_optimization/create_annealing2.sh b/polyamorphism_optimization/create_annealing2.sh
deleted file mode 100755
index b909192..0000000
--- a/polyamorphism_optimization/create_annealing2.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/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 }
-    ' "$file"
-}
-
-simdir="02_an_cooling"
-
-
-rm -r "$simdir" 2>/dev/null
-mkdir "$simdir"
-
-cp topology.top "$simdir/"
-"$(dirname $0)/replace_params.sh" params.ini topology.top --output "$simdir/topology.top"
-"$(dirname $0)/replace_params.sh" params_an1.ini mdp_parameters.mdp --output "$simdir/mdp_parameters.mdp"
-"$(dirname $0)/replace_params.sh" params.ini "$simdir/mdp_parameters.mdp" --output "$simdir/mdp_parameters.mdp"
-cp "$(dirname $0)/run.sh" "$simdir/"
-#cp "00_em/out/out.gro" "$simdir/gro_start.gro"
-
-
-#annealing=$($(dirname $0)/generate_annealing.py -d 50 -l 180 -u 750 -e 2000 -c)
-annealing=$($(dirname $0)/generate_annealing.py -d 20 -l 750 -u 2100 -s 50 -e 10000 -c)
-
-echo "" >> "$simdir/mdp_parameters.mdp"
-echo "$annealing" >> "$simdir/mdp_parameters.mdp"
-
-
diff --git a/polyamorphism_optimization/innitialize_sim.py b/polyamorphism_optimization/innitialize_sim.py
old mode 100644
new mode 100755
diff --git a/polyamorphism_optimization/replace_params.py b/polyamorphism_optimization/replace_params.py
new file mode 100644
index 0000000..cb804e7
--- /dev/null
+++ b/polyamorphism_optimization/replace_params.py
@@ -0,0 +1,41 @@
+#!/usr/bin/env python3
+import sys
+import configparser
+from pathlib import Path
+
+
+def replace_params(param_file: Path, template_file: Path, output_file: Path):
+    """Replace placeholders in template_file with values from an INI file."""
+    config = configparser.ConfigParser()
+    config.optionxform = str  # keep case sensitivity
+    config.read(param_file)
+
+    # Flatten into a simple dict {KEY: VALUE}
+    params = {}
+    for section in config.sections():
+        for key, value in config.items(section):
+            params[key] = value
+
+    content = template_file.read_text()
+
+    for key, value in params.items():
+        content = content.replace(key, value)
+
+    output_file.write_text(content)
+
+
+def main():
+    if len(sys.argv) != 4:
+        print(f"Usage: {sys.argv[0]} PARAM_FILE TEMPLATE_FILE OUTPUT_FILE")
+        sys.exit(1)
+
+    param_file = Path(sys.argv[1])
+    template_file = Path(sys.argv[2])
+    output_file = Path(sys.argv[3])
+
+    replace_params(param_file, template_file, output_file)
+
+
+if __name__ == "__main__":
+    main()
+
diff --git a/polyamorphism_optimization/run.sh b/polyamorphism_optimization/templates/run.sh
similarity index 100%
rename from polyamorphism_optimization/run.sh
rename to polyamorphism_optimization/templates/run.sh
diff --git a/pyproject.toml b/pyproject.toml
index d5caedf..ac4522b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ dependencies = [
 ]
 
 [project.scripts]
-po_setup_sim = "polyamorphism_optimization.setup_sim:main"
+po_init_sim = "polyamorphism_optimization.innitialize_sim:main"
 
 [tool.setuptools.package-data]
 polyamorphism_optimization = ["templates/*"]