diff --git a/dev/CMakeLists.txt b/dev/CMakeLists.txt
index d2fda20a5..8595f165d 100644
--- a/dev/CMakeLists.txt
+++ b/dev/CMakeLists.txt
@@ -82,12 +82,13 @@ include("${DIR_LIBS}/ui/test/cmake/library.cmake")
 
 vtx_clear_registered_copies()
 
-# Tool.
-include("${DIR_LIBS}/tool/cmake/library.cmake")
-
 # MdPrep.
 include("${DIR_LIBS}/tool/tools/mdprep/cmake/library.cmake")
 
 # MdPrep test.
 include("${DIR_LIBS}/tool/tools/mdprep/test/cmake/library.cmake")
 
+# Tool.
+include("${DIR_LIBS}/tool/cmake/library.cmake")
+
+
diff --git a/lib/tool/include/tool/mdprep.hpp b/lib/tool/include/tool/mdprep.hpp
index 896acde22..2959ccb40 100644
--- a/lib/tool/include/tool/mdprep.hpp
+++ b/lib/tool/include/tool/mdprep.hpp
@@ -23,6 +23,13 @@ namespace VTX::Tool
 	  private:
 		void _addButtonsInMenu();
 		void _openMdPrepWindow();
+
+		struct Data;
+		struct Del
+		{
+			void operator()( Data * ) const noexcept;
+		};
+		std::unique_ptr<Data, Del> _data = nullptr;
 	};
 } // namespace VTX::Tool
 
diff --git a/lib/tool/src/tool/mdprep.cpp b/lib/tool/src/tool/mdprep.cpp
index 7d38bcdc6..8f1a9e158 100644
--- a/lib/tool/src/tool/mdprep.cpp
+++ b/lib/tool/src/tool/mdprep.cpp
@@ -1,4 +1,5 @@
 #include "tool/mdprep.hpp"
+#include "tools/mdprep/mdprep.hpp"
 #include "ui/qt/application_qt.hpp"
 #include "ui/qt/main_window.hpp"
 #include "ui/qt/tool/pytx/details/include_python_binding.hpp"
@@ -12,6 +13,11 @@
 namespace VTX::Tool
 {
 
+	struct ToolMdprep::Data
+	{
+		VTX::Tool::Mdprep::MainWindow mainWindow;
+	};
+
 	ToolMdprep::ToolMdprep() {}
 	void ToolMdprep::instantiateTool()
 	{
@@ -32,12 +38,18 @@ namespace VTX::Tool
 			= VTX::UI::QT::WidgetFactory::get().instantiateWidget<VTX::UI::QT::Widget::MainMenu::MenuToolButtonWidget>(
 				&toolBlock, "MdPrepButton"
 			);
-		// button->setData( "MD prep", ":/sprite/info_button.png", Qt::Orientation::Vertical );
 		button->setData( "MD prep", ":/sprite/icon_tool_mdprep_mainButton.png", Qt::Orientation::Vertical );
 		button->setTriggerAction( this, &ToolMdprep::_openMdPrepWindow );
 
 		toolBlock.pushButton( *button );
 	}
-	void ToolMdprep::_openMdPrepWindow() { VTX_INFO( "Opening ToolMdprep window" ); }
+	void ToolMdprep::_openMdPrepWindow()
+	{
+		VTX_INFO( "Opening ToolMdprep window" );
+		_data.reset( new Data() );
+		_data->mainWindow.show();
+	}
+
+	void VTX::Tool::ToolMdprep::Del::operator()( Data * p_ ) const noexcept { delete p_; }
 
 } // namespace VTX::Tool
diff --git a/lib/tool/tools/mdprep/cmake/library.cmake b/lib/tool/tools/mdprep/cmake/library.cmake
index 1544f9852..b63036130 100644
--- a/lib/tool/tools/mdprep/cmake/library.cmake
+++ b/lib/tool/tools/mdprep/cmake/library.cmake
@@ -9,6 +9,7 @@ set(SOURCES "")
 set(QT_FORMS "")
 set(QT_RESOURCES "")
 file(GLOB_RECURSE HEADERS "${CMAKE_CURRENT_LIST_DIR}/../include/*")
+message("mdprep headers : <${HEADERS}>")
 file(GLOB_RECURSE SOURCES "${CMAKE_CURRENT_LIST_DIR}/../src/*")
 file(GLOB_RECURSE QT_FORMS asset/qt/forms/*.ui)
 file(GLOB_RECURSE QT_RESOURCES asset/qt/resources/*.qrc)
@@ -23,10 +24,12 @@ if (NOT DEFINED _VTX_MDPREP_CONAN)
 	target_link_libraries(vtx_tool_mdprep PRIVATE vtx_util)
 	target_link_libraries(vtx_tool_mdprep PRIVATE vtx_core)
 	target_link_libraries(vtx_tool_mdprep PRIVATE vtx_app)
+	target_link_libraries(vtx_tool_mdprep PRIVATE vtx_ui)
 else()
 	target_link_libraries(vtx_tool_mdprep PRIVATE vtx_util::vtx_util)
 	target_link_libraries(vtx_tool_mdprep PRIVATE vtx_core::vtx_core)
 	target_link_libraries(vtx_tool_mdprep PRIVATE vtx_app::vtx_app)
+	target_link_libraries(vtx_tool_mdprep PRIVATE vtx_ui::vtx_ui)
 endif()
 target_link_libraries(vtx_tool_mdprep PRIVATE Qt6::Core)
 target_link_libraries(vtx_tool_mdprep PRIVATE Qt6::Gui)
diff --git a/lib/tool/tools/mdprep/conanfile.py b/lib/tool/tools/mdprep/conanfile.py
index 084066e1b..815c64559 100644
--- a/lib/tool/tools/mdprep/conanfile.py
+++ b/lib/tool/tools/mdprep/conanfile.py
@@ -24,6 +24,7 @@ class VTXToolMdprepRecipe(ConanFile):
     def requirements(self):
         self.requires("vtx_util/1.0")
         self.requires("vtx_app/1.0")
+        self.requires("vtx_core/1.0")
         self.requires("vtx_ui/1.0")
         self.requires("re2/20231101")
         self.requires("gromacs/2024.0")
diff --git a/lib/tool/tools/mdprep/include/tools/mdprep/mdprep.hpp b/lib/tool/tools/mdprep/include/tools/mdprep/mdprep.hpp
index ac5dfbb08..42dcebb06 100644
--- a/lib/tool/tools/mdprep/include/tools/mdprep/mdprep.hpp
+++ b/lib/tool/tools/mdprep/include/tools/mdprep/mdprep.hpp
@@ -1,5 +1,25 @@
+#ifndef __VTX_TOOL_TOOLS_MDPREP__
+#define __VTX_TOOL_TOOLS_MDPREP__
 
+#include <memory>
 
 namespace VTX::Tool::Mdprep
 {
+	// Designed to be the self-contained window that allow the user to use the MDprep tool
+	class MainWindow
+	{
+	  public:
+		MainWindow();
+
+		void show() noexcept;
+
+	  private:
+		class _impl;
+		struct Del
+		{
+			void operator()( _impl * ) noexcept;
+		};
+		std::unique_ptr<_impl, Del> _pimpl = nullptr;
+	};
 } // namespace VTX::Tool::Mdprep
+#endif
diff --git a/lib/tool/tools/mdprep/include/tools/mdprep/ui/main_window.hpp b/lib/tool/tools/mdprep/include/tools/mdprep/ui/main_window.hpp
new file mode 100644
index 000000000..5015b3c8f
--- /dev/null
+++ b/lib/tool/tools/mdprep/include/tools/mdprep/ui/main_window.hpp
@@ -0,0 +1,20 @@
+#ifndef __VTX_TOOL_TOOLS_MDPREP_UI_MAINWINDOW__
+#define __VTX_TOOL_TOOLS_MDPREP_UI_MAINWINDOW__
+
+#include <array>
+#include <string>
+
+namespace VTX::Tool::Mdprep::ui
+{
+	enum class E_MD_ENGINE
+	{
+		gromacs,
+		COUNT
+	};
+	constexpr const size_t MD_ENGINE_NUMBER = static_cast<size_t>( E_MD_ENGINE::COUNT );
+	constexpr const char * string( const E_MD_ENGINE & ) noexcept;
+
+	const std::array<const char *, MD_ENGINE_NUMBER> & mdEngineStrings();
+} // namespace VTX::Tool::Mdprep::ui
+
+#endif
diff --git a/lib/tool/tools/mdprep/src/mdprep.cpp b/lib/tool/tools/mdprep/src/mdprep.cpp
index b2a9282b6..de3ee280a 100644
--- a/lib/tool/tools/mdprep/src/mdprep.cpp
+++ b/lib/tool/tools/mdprep/src/mdprep.cpp
@@ -1,6 +1,81 @@
 #include "tools/mdprep/mdprep.hpp"
+#include "tools/mdprep/ui/main_window.hpp"
+#include <qcombobox.h>
+#include <qformlayout.h>
+#include <qlineedit.h>
+#include <ui/qt/application_qt.hpp>
+#include <ui/qt/main_window.hpp>
+#include <util/logger.hpp>
+
+namespace VTX::QT::Mdprep
+{
+	class MainWindow : public UI::QT::QtDockablePanel
+	{
+	  private:
+		inline static const QSize PREFERRED_SIZE { 640, 720 };
+		virtual void			  _setupUi( const QString & p_name )
+		{
+			auto		_t = p_name.toLatin1();
+			std::string v( _t.begin(), _t.end() );
+			VTX::VTX_INFO( "info from Mdprep::MainWindow::_setupUi : <{}>", v );
+			QWidget * const mainWidget = _instantiateMainWidget( PREFERRED_SIZE, PREFERRED_SIZE );
+
+			UI::QT::QtDockablePanel::_setupUi( p_name );
+
+			this->setWindowTitle( "Molecular Dynamics Preparation" );
+
+			setWindowState( Qt::WindowState::WindowActive );
+			const QSize winsize = QSize( 640, 720 );
+			resize( winsize );
+
+			QVBoxLayout * windowLayout = new QVBoxLayout( mainWidget );
+			windowLayout->setContentsMargins( 0, 0, 0, 0 );
+
+			QComboBox * engineList = new QComboBox;
+			for ( auto & it : VTX::Tool::Mdprep::ui::mdEngineStrings() )
+				engineList->addItem( QString( it ) );
+
+			QWidget * mainContainer = new QWidget( this );
+			mainContainer->setStyleSheet( "border: 1px solid red" );
+			mainContainer->setSizePolicy( QSizePolicy( QSizePolicy ::Expanding, QSizePolicy ::Expanding ) );
+			windowLayout->addWidget( mainContainer, 1 );
+			QHBoxLayout * hLayout = new QHBoxLayout( mainContainer );
+
+			auto layoutToAddThoseTextboxTo = hLayout;
+
+			QLineEdit * textbox = new QLineEdit();
+			textbox->setText( "textbox" );
+			// QFormLayout * layout = new QFormLayout( this );
+			// layout->addRow( tr( "&Textbox:" ), textbox );
+			// layout->addRow( tr( "&Textbox2:" ), textbox2 );
+			// hLayout->addLayout( layout );
+			layoutToAddThoseTextboxTo->addWidget( engineList, 1 );
+			layoutToAddThoseTextboxTo->addWidget( textbox, 1 );
+		}
+		virtual void _setupSlots() { VTX::VTX_INFO( "info from Mdprep::MainWindow::_setupSlots" ); }
+
+	  public:
+		MainWindow( QWidget * const p_parent = nullptr ) : UI::QT::QtDockablePanel( p_parent )
+		{
+			_setupUi( "Is this parameter useful ?" );
+		}
+	};
+} // namespace VTX::QT::Mdprep
 
 namespace VTX::Tool::Mdprep
 {
 
+	class MainWindow::_impl
+	{
+		VTX::QT::Mdprep::MainWindow _win { &VTX::UI::QT::QT_APP()->getMainWindow() };
+
+	  public:
+		_impl() {}
+		void show() noexcept { _win.show(); }
+	};
+	MainWindow::MainWindow() : _pimpl( new MainWindow::_impl() ) {}
+
+	// Assumes pimpl is always valid ptr
+	void MainWindow::show() noexcept { _pimpl->show(); }
+	void MainWindow::Del::operator()( _impl * p_ ) noexcept { delete p_; }
 } // namespace VTX::Tool::Mdprep
diff --git a/lib/tool/tools/mdprep/src/ui/main_window.cpp b/lib/tool/tools/mdprep/src/ui/main_window.cpp
new file mode 100644
index 000000000..5942bed54
--- /dev/null
+++ b/lib/tool/tools/mdprep/src/ui/main_window.cpp
@@ -0,0 +1,29 @@
+#include "tools/mdprep/ui/main_window.hpp"
+
+namespace VTX::Tool::Mdprep::ui
+{
+	constexpr const char * string( const E_MD_ENGINE & p_ ) noexcept
+	{
+		switch ( p_ )
+		{
+		case E_MD_ENGINE::gromacs: return { "Gromacs" };
+		default: break;
+		}
+		return "Please provide a user string for the MD engine"; // For developers that add new MD Engine support
+	}
+	namespace
+	{
+		constexpr std::array<const char *, MD_ENGINE_NUMBER> createMdEngineStringList()
+		{
+			std::array<const char *, MD_ENGINE_NUMBER> out;
+			for ( int i = 0; i < MD_ENGINE_NUMBER; i++ )
+			{
+				out[ i ] = string( static_cast<E_MD_ENGINE>( i ) );
+			}
+			return out;
+		}
+	} // namespace
+	constexpr const std::array<const char *, MD_ENGINE_NUMBER> g_mdEngineStrings = createMdEngineStringList();
+
+	const std::array<const char *, MD_ENGINE_NUMBER> & mdEngineStrings() { return g_mdEngineStrings; }
+} // namespace VTX::Tool::Mdprep::ui