diff --git a/java/org/contikios/cooja/LogScriptEngine.java b/java/org/contikios/cooja/LogScriptEngine.java
index dd4ce7fbe..8b8ab762d 100644
--- a/java/org/contikios/cooja/LogScriptEngine.java
+++ b/java/org/contikios/cooja/LogScriptEngine.java
@@ -108,9 +108,6 @@ public void removedLogOutput(LogOutputEvent ev) {
   private Thread scriptThread = null; /* Script thread */
   private final Simulation simulation;
 
-  private long timeout;
-  private long startTime;
-  private long startRealTime;
   private final JTextArea textArea;
 
   protected LogScriptEngine(Simulation simulation, int logNumber, JTextArea logTextArea) {
@@ -196,10 +193,7 @@ protected void closeLog() {
    * Deactivate script
    */
   public void deactivateScript() {
-    timeoutProgressEvent.remove();
-
     engine.put("SHUTDOWN", true);
-
     try {
       if (semaphoreScript != null) {
         semaphoreScript.release(100);
@@ -233,7 +227,7 @@ public void deactivateScript() {
    *  Does not alter internal engine state that is difficult to undo. */
   public CompiledScript compileScript(String code) throws ScriptException {
     ScriptParser parser = new ScriptParser(code);
-    timeout = parser.getTimeoutTime();
+    var timeout = parser.getTimeoutTime();
     if (timeout < 0) {
       timeout = DEFAULT_TIMEOUT;
     }
@@ -288,26 +282,9 @@ public boolean activateScript(final CompiledScript script) {
       deactivateScript();
       return false;
     }
-    startRealTime = System.currentTimeMillis();
-    startTime = simulation.getSimulationTime();
-    simulation.invokeSimulationThread(() ->
-            simulation.scheduleEvent(timeoutProgressEvent, startTime + Math.max(1000, timeout / 20)));
     return true;
   }
 
-  private final TimeEvent timeoutProgressEvent = new TimeEvent() {
-    @Override
-    public void execute(long t) {
-      simulation.scheduleEvent(this, t + Math.max(1000, timeout / 20));
-
-      double progress = 1.0*(t - startTime)/timeout;
-      long realDuration = System.currentTimeMillis()-startRealTime;
-      double estimatedLeft = 1.0*realDuration/progress - realDuration;
-      if (estimatedLeft == 0) estimatedLeft = 1;
-      logger.info(String.format("%2.0f%% completed, %2.1f sec remaining", 100*progress, estimatedLeft/1000));
-    }
-  };
-
   private final ScriptLog scriptLog = new ScriptLog() {
     @Override
     public void log(String msg) {
diff --git a/java/org/contikios/cooja/Simulation.java b/java/org/contikios/cooja/Simulation.java
index 4eed0ad21..eb558d0ac 100644
--- a/java/org/contikios/cooja/Simulation.java
+++ b/java/org/contikios/cooja/Simulation.java
@@ -132,6 +132,18 @@ public record MoteRelation(Mote source, Mote dest, Color color) {}
   private final EventTriggers<AddRemove, MoteRelation> moteRelationsTriggers = new EventTriggers<>();
   private final SimConfig cfg;
 
+  private final TimeEvent progressEvent = new TimeEvent() {
+    @Override
+    public void execute(long t) {
+      scheduleEvent(this, t + Math.max(1000, timeout / 20));
+      double progress = 1.0 * (t - lastStartSimulationTime) / timeout;
+      long realDuration = System.currentTimeMillis() - lastStartRealTime;
+      double estimatedLeft = 1.0 * realDuration / progress - realDuration;
+      if (estimatedLeft == 0) estimatedLeft = 1;
+      logger.info(String.format("%2.0f%% completed, %2.1f sec remaining", 100 * progress, estimatedLeft / 1000));
+    }
+  };
+
   private final TimeEvent delayEvent = new TimeEvent() {
     @Override
     public void execute(long t) {
@@ -538,8 +550,11 @@ public void removeScriptEngine(LogScriptEngine engine) {
 
   /** Set the timeout for the simulation. There is no timeout by default. */
   public void setTimeout(long timeout) {
-    this.timeout = timeout;
-    logger.info("Simulation timeout in " + (timeout / MILLISECOND) + " ms");
+    invokeSimulationThread(() -> {
+      this.timeout = timeout;
+      logger.info("Simulation timeout in " + (timeout / MILLISECOND) + " ms");
+      scheduleEvent(progressEvent, currentSimulationTime + Math.max(1000, timeout / 20));
+    });
   }
 
   /**