add gromacs install example script

compile_gromacs_2018.8_bookworm.patch

@@ -0,0 +1,10 @@
+--- gromacs-2018.8/src/gromacs/utility/arrayref.h	2019-10-04 08:39:25.000000000 +0200
++++ gromacs-2018.8-fixed/src/gromacs/utility/arrayref.h	2025-05-23 14:54:03.458763669 +0200
+@@ -46,6 +46,7 @@
+ #include <cstddef>
+ 
+ #include <array>
++#include <limits>
+ #include <iterator>
+ #include <stdexcept>
+ #include <utility>

install_gromacs_2018.8_bookworm.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+
+#set -x
+GMX_VERSION=2018.8
+
+WORKDIR=$PWD
+CMAKE_PARAMETERS="-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-${GMX_VERSION} -DGMX_HWLOC=off"
+
+if [ -f /var/lib/install_gromacs-${GMX_VERSION} ]; then
+	CMAKE_PARAMTERS_OLD=$(</var/lib/install_gromacs-${GMX_VERSION})
+	if [ "$CMAKE_PARAMETERS" == "$CMAKE_PARAMTERS_OLD" ]; then
+		NO_CHANGE=true
+		echo "No change detected"
+	else
+		NO_CHANGE=false
+		echo "Change detected"
+	fi
+else
+	NO_CHANGE=false
+	echo "Change detected, /var/lib/install_gromacs-${GMX_VERSION} not found"
+fi
+
+
+# if the former cmake parameters are the same
+if [ -d /usr/local/gromacs-${GMX_VERSION} -a $NO_CHANGE = true ]; then
+	echo "Assume $GMX_VERSION is installed"
+	exit 0
+else
+	cd /tmp
+	curl --fail https://ftp.gromacs.org/gromacs/gromacs-${GMX_VERSION}.tar.gz \
+		--output gromacs-${GMX_VERSION}.tar.gz \
+		--silent || echo "Version not found: gromacs-${GMX_VERSION}"
+	tar xfz gromacs-${GMX_VERSION}.tar.gz
+	rm gromacs-${GMX_VERSION}.tar.gz
+	mkdir -p gromacs-${GMX_VERSION}/build
+	# this patch is need because 2018.8 is *really* old by now
+	if [ $GMX_VERSION==2018.8 ]; then
+     	    pushd gromacs-${GMX_VERSION}
+	    patch --verbose -p1 < $WORKDIR/compile_gromacs_2018.8_bookworm.patch
+	fi
+	popd
+	pushd gromacs-${GMX_VERSION}/build
+	cmake .. $CMAKE_PARAMETERS
+	make -j $(nproc)
+	make install -j $(nproc)
+	popd
+	rm -rf gromacs-${GMX_VERSION}
+	# save parameters of installation
+	echo $CMAKE_PARAMETERS > /var/lib/install_gromacs-${GMX_VERSION}
+fi
+echo "Run the following command to set the LD_LIBRARY_PATH in order to compile pygmx:"
+echo "source /usr/local/gromacs-${GMX_VERSION}/bin/GMXRC"