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/usr/share/gromacs/template/Makefile.pkg is in libgromacs-dev 5.1.2-1ubuntu1.

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The actual contents of the file can be viewed below.

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# This is a GROMACS template makefile for your own utility programs using pkg-config.
#
# Copy this file to whatever directory you are using for your own software
#
# Usage:
# $ source /path/to/GMXRC
# $ make -f Makefile.pkg
#
#change the name of the program here
NAME=template

#add extra c++ file(s) to compile here
EXTRA_SRC=

###############################################################3
#below only boring default stuff
#only change it if you know what you are doing ;-)

#what should be done by default
all: $(NAME)

#if GMXLDLIB is defined we add it to PKG_CONFIG_PATH
ifeq "$(origin GMXLDLIB)" "undefined"
  $(error "GMXLDLIB not found, please source GMXRC")
else
  export PKG_CONFIG_PATH:=${PKG_CONFIG_PATH}:${GMXLDLIB}/pkgconfig
endif

#get CPPFLAGS and LDFLAGS from pkg-config
CPPFLAGS=`pkg-config --cflags libgromacs`
LDFLAGS=`pkg-config --libs libgromacs`

#generate a list of object (.o) files
OBJS=$(patsubst %.cpp,%.o,$(NAME).cpp $(EXTRA_SRC))

#main program depend on all objects, rest is done by implicit rules
$(NAME): $(OBJS)
	$(CXX) $(LDFLAGS) -o $@ $^

#clean up rule
clean:
	rm -f $(NAME) $(OBJS)

#all, clean are phony rules, e.g. they are always run
.PHONY: all clean