diff --git a/PuReMD/Makefile.am b/PuReMD/Makefile.am
index 718c453fa84b45f83c4c3890eda1735fbb0b7f20..c657b37a7bde1349eaa877de14d82b8d8bf727cd 100644
--- a/PuReMD/Makefile.am
+++ b/PuReMD/Makefile.am
@@ -6,9 +6,8 @@ bin_puremd_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c src
       src/vector.c src/analyze.c src/box.c src/system_props.c src/control.c src/comm_tools.c \
       src/geo_tools.c src/linear_solvers.c src/neighbors.c src/qEq.c src/bond_orders.c src/multi_body.c \
       src/bonds.c src/valence_angles.c src/hydrogen_bonds.c src/torsion_angles.c src/nonbonded.c src/forces.c \
-      src/integrate.c src/init_md.c src/parallelreax.c
-
-include_HEADERS = src/reax_defs.h src/reax_types.h \
+      src/integrate.c src/init_md.c src/parallelreax.c \
+      src/reax_defs.h src/reax_types.h \
       src/allocate.h src/basic_comm.h src/ffield.h src/grid.h src/list.h src/lookup.h \
       src/io_tools.h src/reset_tools.h src/restart.h src/random.h src/tool_box.h src/traj.h \
       src/vector.h src/analyze.h src/box.h src/system_props.h src/control.h src/comm_tools.h \
@@ -16,5 +15,5 @@ include_HEADERS = src/reax_defs.h src/reax_types.h \
       src/bonds.h src/valence_angles.h src/hydrogen_bonds.h src/torsion_angles.h src/nonbonded.h src/forces.h \
       src/integrate.h src/init_md.h
 
-bin_puremd_CFLAGS = $(CFLAGS) $(MPI_CFLAGS)
-bin_puremd_LDADD = $(LDADD) $(MPI_LIBS)
+bin_puremd_CFLAGS = $(MPI_CFLAGS)
+bin_puremd_LDADD = $(MPI_LIBS)
diff --git a/PuReMD/configure.ac b/PuReMD/configure.ac
index 8833fc248a64e49a684106feeaeb4682c54bf715..6a1bb0a187736d4baf0207f537e2d224758a3901 100644
--- a/PuReMD/configure.ac
+++ b/PuReMD/configure.ac
@@ -74,7 +74,6 @@ fi
 CONFIGURE_HEADLINE([ MPI compiler ])
 ACX_MPI([], [AC_MSG_ERROR([could not find mpi library])])
 AC_CHECK_PROG(MPIRUN, mpirun, mpirun)
-AC_SUBST(MPIRUN)
 
 # try to find if we are using OpenMPI / MPICH by looking inside mpi.h
 save_CC="${CC}"
diff --git a/configure.ac b/configure.ac
index 95a0443651267cfed80e6c99245af81a209f7925..830a2ce26a6b8bce71fccc7c059593fa2b7aafb2 100644
--- a/configure.ac
+++ b/configure.ac
@@ -84,9 +84,7 @@ if test "x${DEBUG}" = "xyes"
 then
 #	#TODO: fix exporting to subdirs
 #	# See: http://stackoverflow.com/questions/34124337/changing-flags-in-configure-ac-vs-caching-with-subprojects
-#	CFLAGS="-g3 -O0 -D_GLIBCXX_DEBUG ${CFLAGS}"
-	export BUILD_DEBUG="true"
-	export DEBUG_FLAGS="-g2 -O0 -D_GLIBCXX_DEBUG"
+	export BUILD_DEBUG="yes"
 fi
 
 # gprof flags.