From: Teemu Murtola <teemu.murtola@gmail.com>
Date: Sat, 6 Sep 2014 16:43:24 +0000 (+0300)
Subject: Sort all includes in src/gromacs
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?p=alexxy%2Fgromacs.git;a=commitdiff_plain;h=30692f54df98c3e8612dfdb1aa288ed51a7444b3

Sort all includes in src/gromacs

Used:
  admin/reformat_all.sh --pattern=src/gromacs includesort -B=../build
after building the doc-check target (whose dependencies are needed for
the sorter).

Change-Id: Icde0fb5cb5bc082fb4381d4cba1211329bad3fa5
---

diff --git a/src/gromacs/analysisdata.h b/src/gromacs/analysisdata.h
index 51f2d44156..0bea920364 100644
--- a/src/gromacs/analysisdata.h
+++ b/src/gromacs/analysisdata.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -201,13 +201,13 @@
 #ifndef GMX_ANALYSISDATA_H
 #define GMX_ANALYSISDATA_H
 
-#include "analysisdata/analysisdata.h"
-#include "analysisdata/arraydata.h"
-#include "analysisdata/dataframe.h"
-#include "analysisdata/modules/average.h"
-#include "analysisdata/modules/displacement.h"
-#include "analysisdata/modules/histogram.h"
-#include "analysisdata/modules/lifetime.h"
-#include "analysisdata/modules/plot.h"
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/analysisdata/modules/average.h"
+#include "gromacs/analysisdata/modules/displacement.h"
+#include "gromacs/analysisdata/modules/histogram.h"
+#include "gromacs/analysisdata/modules/lifetime.h"
+#include "gromacs/analysisdata/modules/plot.h"
 
 #endif
diff --git a/src/gromacs/analysisdata/abstractdata.cpp b/src/gromacs/analysisdata/abstractdata.cpp
index bdc43b4536..9d21ccad6c 100644
--- a/src/gromacs/analysisdata/abstractdata.cpp
+++ b/src/gromacs/analysisdata/abstractdata.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/abstractdata.h"
+#include "abstractdata.h"
 
 #include <vector>
 
diff --git a/src/gromacs/analysisdata/abstractdata.h b/src/gromacs/analysisdata/abstractdata.h
index 6a122f58e2..07dc2ed0e4 100644
--- a/src/gromacs/analysisdata/abstractdata.h
+++ b/src/gromacs/analysisdata/abstractdata.h
@@ -45,7 +45,7 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/analysisdata.cpp b/src/gromacs/analysisdata/analysisdata.cpp
index 1d9f023999..300b2bd56f 100644
--- a/src/gromacs/analysisdata/analysisdata.cpp
+++ b/src/gromacs/analysisdata/analysisdata.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/analysisdata.h"
+#include "analysisdata.h"
 
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datastorage.h"
diff --git a/src/gromacs/analysisdata/analysisdata.h b/src/gromacs/analysisdata/analysisdata.h
index 4de2c116bb..b8849769ea 100644
--- a/src/gromacs/analysisdata/analysisdata.h
+++ b/src/gromacs/analysisdata/analysisdata.h
@@ -43,9 +43,8 @@
 #ifndef GMX_ANALYSISDATA_ANALYSISDATA_H
 #define GMX_ANALYSISDATA_ANALYSISDATA_H
 
-#include "../utility/real.h"
-
-#include "abstractdata.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/arraydata.cpp b/src/gromacs/analysisdata/arraydata.cpp
index 6124ce6d67..60d4c89cfd 100644
--- a/src/gromacs/analysisdata/arraydata.cpp
+++ b/src/gromacs/analysisdata/arraydata.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/arraydata.h"
+#include "arraydata.h"
 
 #include <algorithm>
 
diff --git a/src/gromacs/analysisdata/arraydata.h b/src/gromacs/analysisdata/arraydata.h
index 71efadf6ed..f255ae70f6 100644
--- a/src/gromacs/analysisdata/arraydata.h
+++ b/src/gromacs/analysisdata/arraydata.h
@@ -45,10 +45,9 @@
 
 #include <vector>
 
-#include "../utility/gmxassert.h"
-
-#include "abstractdata.h"
-#include "dataframe.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/dataframe.h b/src/gromacs/analysisdata/dataframe.h
index b5d0da65e6..5502063042 100644
--- a/src/gromacs/analysisdata/dataframe.h
+++ b/src/gromacs/analysisdata/dataframe.h
@@ -45,10 +45,10 @@
 
 #include <vector>
 
-#include "../utility/arrayref.h"
-#include "../utility/flags.h"
-#include "../utility/gmxassert.h"
-#include "../utility/real.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/flags.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/datamodule.cpp b/src/gromacs/analysisdata/datamodule.cpp
index 694aeff0e8..dde3922dbd 100644
--- a/src/gromacs/analysisdata/datamodule.cpp
+++ b/src/gromacs/analysisdata/datamodule.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/datamodule.h"
+#include "datamodule.h"
 
 #include "gromacs/analysisdata/paralleloptions.h"
 
diff --git a/src/gromacs/analysisdata/datamodulemanager.cpp b/src/gromacs/analysisdata/datamodulemanager.cpp
index 3a22614b7d..5946a4f637 100644
--- a/src/gromacs/analysisdata/datamodulemanager.cpp
+++ b/src/gromacs/analysisdata/datamodulemanager.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/datamodulemanager.h"
+#include "datamodulemanager.h"
 
 #include <vector>
 
diff --git a/src/gromacs/analysisdata/datamodulemanager.h b/src/gromacs/analysisdata/datamodulemanager.h
index 81ebbbbeee..4688ce01b3 100644
--- a/src/gromacs/analysisdata/datamodulemanager.h
+++ b/src/gromacs/analysisdata/datamodulemanager.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,9 +43,8 @@
 #ifndef GMX_ANALYSISDATA_DATAMODULEMANAGER_H
 #define GMX_ANALYSISDATA_DATAMODULEMANAGER_H
 
-#include "abstractdata.h"
-
-#include "../utility/common.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/dataproxy.h b/src/gromacs/analysisdata/dataproxy.h
index 50f6d52d5b..d4c6af3b8f 100644
--- a/src/gromacs/analysisdata/dataproxy.h
+++ b/src/gromacs/analysisdata/dataproxy.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,8 +45,8 @@
 #ifndef GMX_ANALYSISDATA_DATAPROXY_H
 #define GMX_ANALYSISDATA_DATAPROXY_H
 
-#include "abstractdata.h"
-#include "datamodule.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/datamodule.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/datastorage.h b/src/gromacs/analysisdata/datastorage.h
index 9c32aa8c8f..8fd2b00ff0 100644
--- a/src/gromacs/analysisdata/datastorage.h
+++ b/src/gromacs/analysisdata/datastorage.h
@@ -45,11 +45,10 @@
 
 #include <vector>
 
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-#include "../utility/real.h"
-
-#include "dataframe.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/modules/average.h b/src/gromacs/analysisdata/modules/average.h
index 3f8f583f06..558ee1e57b 100644
--- a/src/gromacs/analysisdata/modules/average.h
+++ b/src/gromacs/analysisdata/modules/average.h
@@ -45,10 +45,10 @@
 
 #include <vector>
 
-#include "../abstractdata.h"
-#include "../arraydata.h"
-#include "../datamodule.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/modules/displacement.cpp b/src/gromacs/analysisdata/modules/displacement.cpp
index 1320d40eaf..9b9b2f468d 100644
--- a/src/gromacs/analysisdata/modules/displacement.cpp
+++ b/src/gromacs/analysisdata/modules/displacement.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/modules/displacement.h"
+#include "displacement.h"
 
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datamodulemanager.h"
diff --git a/src/gromacs/analysisdata/modules/displacement.h b/src/gromacs/analysisdata/modules/displacement.h
index 88cac9ba50..398acf11ad 100644
--- a/src/gromacs/analysisdata/modules/displacement.h
+++ b/src/gromacs/analysisdata/modules/displacement.h
@@ -43,10 +43,9 @@
 #ifndef GMX_ANALYSISDATA_MODULES_DISPLACEMENT_H
 #define GMX_ANALYSISDATA_MODULES_DISPLACEMENT_H
 
-#include "../../utility/real.h"
-
-#include "../abstractdata.h"
-#include "../datamodule.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/modules/frameaverager.h b/src/gromacs/analysisdata/modules/frameaverager.h
index 7531abeb5d..61867c24c4 100644
--- a/src/gromacs/analysisdata/modules/frameaverager.h
+++ b/src/gromacs/analysisdata/modules/frameaverager.h
@@ -44,8 +44,8 @@
 
 #include <vector>
 
-#include "../../utility/gmxassert.h"
-#include "../../utility/real.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/modules/histogram.cpp b/src/gromacs/analysisdata/modules/histogram.cpp
index 48df0079f7..cc9c601e96 100644
--- a/src/gromacs/analysisdata/modules/histogram.cpp
+++ b/src/gromacs/analysisdata/modules/histogram.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/modules/histogram.h"
+#include "histogram.h"
 
 #include <cmath>
 
diff --git a/src/gromacs/analysisdata/modules/histogram.h b/src/gromacs/analysisdata/modules/histogram.h
index c577dae07d..280c4784f7 100644
--- a/src/gromacs/analysisdata/modules/histogram.h
+++ b/src/gromacs/analysisdata/modules/histogram.h
@@ -45,9 +45,9 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../abstractdata.h"
-#include "../arraydata.h"
-#include "../datamodule.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/modules/lifetime.h b/src/gromacs/analysisdata/modules/lifetime.h
index 64560fdcdb..128fbfc053 100644
--- a/src/gromacs/analysisdata/modules/lifetime.h
+++ b/src/gromacs/analysisdata/modules/lifetime.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,9 +43,9 @@
 #ifndef GMX_ANALYSISDATA_MODULES_LIFETIME_H
 #define GMX_ANALYSISDATA_MODULES_LIFETIME_H
 
-#include "../arraydata.h"
-#include "../datamodule.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/modules/plot.cpp b/src/gromacs/analysisdata/modules/plot.cpp
index 9ef70050f5..e421e2d64a 100644
--- a/src/gromacs/analysisdata/modules/plot.cpp
+++ b/src/gromacs/analysisdata/modules/plot.cpp
@@ -41,21 +41,20 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/analysisdata/modules/plot.h"
-
-#include <string>
-#include <vector>
+#include "plot.h"
 
 #include <cstdio>
 #include <cstring>
 
-#include <boost/shared_ptr.hpp>
+#include <string>
+#include <vector>
 
-#include "gromacs/legacyheaders/oenv.h"
+#include <boost/shared_ptr.hpp>
 
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
diff --git a/src/gromacs/analysisdata/modules/plot.h b/src/gromacs/analysisdata/modules/plot.h
index 916fa4a151..9696d54e66 100644
--- a/src/gromacs/analysisdata/modules/plot.h
+++ b/src/gromacs/analysisdata/modules/plot.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,9 +47,9 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../datamodule.h"
-#include "../../options/timeunitmanager.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/analysisdata/tests/analysisdata.cpp b/src/gromacs/analysisdata/tests/analysisdata.cpp
index d8949f6c8a..7cdd8baffa 100644
--- a/src/gromacs/analysisdata/tests/analysisdata.cpp
+++ b/src/gromacs/analysisdata/tests/analysisdata.cpp
@@ -47,10 +47,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/analysisdata/analysisdata.h"
+
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/paralleloptions.h"
 #include "gromacs/utility/exceptions.h"
 
diff --git a/src/gromacs/analysisdata/tests/arraydata.cpp b/src/gromacs/analysisdata/tests/arraydata.cpp
index eec3aa3f08..56b73ecedf 100644
--- a/src/gromacs/analysisdata/tests/arraydata.cpp
+++ b/src/gromacs/analysisdata/tests/arraydata.cpp
@@ -46,10 +46,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/analysisdata/arraydata.h"
 
+#include <gtest/gtest.h>
+
 #include "gromacs/analysisdata/tests/datatest.h"
 #include "testutils/testasserts.h"
 
diff --git a/src/gromacs/analysisdata/tests/average.cpp b/src/gromacs/analysisdata/tests/average.cpp
index 64d3eeccdd..cbfc91cd2a 100644
--- a/src/gromacs/analysisdata/tests/average.cpp
+++ b/src/gromacs/analysisdata/tests/average.cpp
@@ -48,10 +48,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/analysisdata/modules/average.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/average.h"
 
 #include "gromacs/analysisdata/tests/datatest.h"
 #include "testutils/testasserts.h"
diff --git a/src/gromacs/analysisdata/tests/histogram.cpp b/src/gromacs/analysisdata/tests/histogram.cpp
index baf6774786..491568b49f 100644
--- a/src/gromacs/analysisdata/tests/histogram.cpp
+++ b/src/gromacs/analysisdata/tests/histogram.cpp
@@ -48,10 +48,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/analysisdata/modules/histogram.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/histogram.h"
 
 #include "gromacs/analysisdata/tests/datatest.h"
 #include "testutils/testasserts.h"
diff --git a/src/gromacs/analysisdata/tests/lifetime.cpp b/src/gromacs/analysisdata/tests/lifetime.cpp
index c154213922..7364b1c7d5 100644
--- a/src/gromacs/analysisdata/tests/lifetime.cpp
+++ b/src/gromacs/analysisdata/tests/lifetime.cpp
@@ -47,10 +47,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/analysisdata/modules/lifetime.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/lifetime.h"
 
 #include "gromacs/analysisdata/tests/datatest.h"
 #include "testutils/testasserts.h"
diff --git a/src/gromacs/bonded/bonded.cpp b/src/gromacs/bonded/bonded.cpp
index 0ad3139599..481c34ae8a 100644
--- a/src/gromacs/bonded/bonded.cpp
+++ b/src/gromacs/bonded/bonded.cpp
@@ -41,22 +41,23 @@
 #include "config.h"
 
 #include <assert.h>
+
 #include <cmath>
 
 #include <algorithm>
 
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/bonded/restcbt.h"
 #include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
 #include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
@@ -66,8 +67,6 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "restcbt.h"
-
 /* Find a better place for this? */
 const int cmap_coeff_matrix[] = {
     1, 0, -3,  2, 0, 0,  0,  0, -3,  0,  9, -6,  2,  0, -6,  4,
diff --git a/src/gromacs/bonded/bonded.h b/src/gromacs/bonded/bonded.h
index 542f579767..0fdc81d9fc 100644
--- a/src/gromacs/bonded/bonded.h
+++ b/src/gromacs/bonded/bonded.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/bonded/restcbt.h b/src/gromacs/bonded/restcbt.h
index 9f2490c19b..66a5f96fde 100644
--- a/src/gromacs/bonded/restcbt.h
+++ b/src/gromacs/bonded/restcbt.h
@@ -52,8 +52,8 @@
 #define GMX_BONDED_RESTCBT_H
 
 #include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/topology/idef.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/topology/idef.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/commandline.h b/src/gromacs/commandline.h
index d29ba2668f..eeba8f3ab3 100644
--- a/src/gromacs/commandline.h
+++ b/src/gromacs/commandline.h
@@ -78,10 +78,10 @@
 #ifndef GMX_COMMANDLINE_H
 #define GMX_COMMANDLINE_H
 
-#include "commandline/cmdlinehelpwriter.h"
-#include "commandline/cmdlineinit.h"
-#include "commandline/cmdlinemodule.h"
-#include "commandline/cmdlineparser.h"
-#include "commandline/pargs.h"
+#include "gromacs/commandline/cmdlinehelpwriter.h"
+#include "gromacs/commandline/cmdlineinit.h"
+#include "gromacs/commandline/cmdlinemodule.h"
+#include "gromacs/commandline/cmdlineparser.h"
+#include "gromacs/commandline/pargs.h"
 
 #endif
diff --git a/src/gromacs/commandline/cmdlinehelpcontext.cpp b/src/gromacs/commandline/cmdlinehelpcontext.cpp
index e90ede652c..e98997e5bf 100644
--- a/src/gromacs/commandline/cmdlinehelpcontext.cpp
+++ b/src/gromacs/commandline/cmdlinehelpcontext.cpp
@@ -43,9 +43,10 @@
 
 #include "cmdlinehelpcontext.h"
 
-#include "gromacs/commandline/shellcompletions.h"
 #include "gromacs/utility/gmxassert.h"
 
+#include "shellcompletions.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/commandline/cmdlinehelpcontext.h b/src/gromacs/commandline/cmdlinehelpcontext.h
index 154facabab..57aa7363c3 100644
--- a/src/gromacs/commandline/cmdlinehelpcontext.h
+++ b/src/gromacs/commandline/cmdlinehelpcontext.h
@@ -43,8 +43,8 @@
 #ifndef GMX_COMMANDLINE_CMDLINEHELPCONTEXT_H
 #define GMX_COMMANDLINE_CMDLINEHELPCONTEXT_H
 
-#include "../onlinehelp/helpwritercontext.h"
-#include "../utility/common.h"
+#include "gromacs/onlinehelp/helpwritercontext.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/commandline/cmdlinehelpmodule.cpp b/src/gromacs/commandline/cmdlinehelpmodule.cpp
index 585413df04..3a67a1ff4a 100644
--- a/src/gromacs/commandline/cmdlinehelpmodule.cpp
+++ b/src/gromacs/commandline/cmdlinehelpmodule.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/commandline/cmdlinehelpmodule.h"
+#include "cmdlinehelpmodule.h"
 
 #include <string>
 #include <vector>
@@ -51,7 +51,6 @@
 #include "gromacs/commandline/cmdlinehelpcontext.h"
 #include "gromacs/commandline/cmdlinehelpwriter.h"
 #include "gromacs/commandline/cmdlineparser.h"
-#include "gromacs/commandline/shellcompletions.h"
 #include "gromacs/onlinehelp/helpformat.h"
 #include "gromacs/onlinehelp/helpmanager.h"
 #include "gromacs/onlinehelp/helptopic.h"
@@ -65,6 +64,8 @@
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "shellcompletions.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/commandline/cmdlinehelpmodule.h b/src/gromacs/commandline/cmdlinehelpmodule.h
index 9fa23b9f31..6b6d33413c 100644
--- a/src/gromacs/commandline/cmdlinehelpmodule.h
+++ b/src/gromacs/commandline/cmdlinehelpmodule.h
@@ -42,12 +42,12 @@
 #ifndef GMX_COMMANDLINE_CMDLINEHELPMODULE_H
 #define GMX_COMMANDLINE_CMDLINEHELPMODULE_H
 
-#include "cmdlinemodule.h"
-#include "cmdlinemodulemanager-impl.h"
-
+#include "gromacs/commandline/cmdlinemodule.h"
 #include "gromacs/onlinehelp/helptopicinterface.h"
 #include "gromacs/utility/common.h"
 
+#include "cmdlinemodulemanager-impl.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/commandline/cmdlinehelpwriter.cpp b/src/gromacs/commandline/cmdlinehelpwriter.cpp
index b410e904af..0c79bd3934 100644
--- a/src/gromacs/commandline/cmdlinehelpwriter.cpp
+++ b/src/gromacs/commandline/cmdlinehelpwriter.cpp
@@ -51,7 +51,6 @@
 #include <boost/scoped_ptr.hpp>
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/shellcompletions.h"
 #include "gromacs/onlinehelp/helpformat.h"
 #include "gromacs/onlinehelp/helpwritercontext.h"
 #include "gromacs/options/basicoptions.h"
@@ -64,6 +63,8 @@
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "shellcompletions.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/commandline/cmdlinehelpwriter.h b/src/gromacs/commandline/cmdlinehelpwriter.h
index 1ab3add952..3ffd581c7e 100644
--- a/src/gromacs/commandline/cmdlinehelpwriter.h
+++ b/src/gromacs/commandline/cmdlinehelpwriter.h
@@ -43,7 +43,7 @@
 #ifndef GMX_COMMANDLINE_CMDLINEHELPWRITER_H
 #define GMX_COMMANDLINE_CMDLINEHELPWRITER_H
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/commandline/cmdlineinit.cpp b/src/gromacs/commandline/cmdlineinit.cpp
index 853901386c..8fe171ee05 100644
--- a/src/gromacs/commandline/cmdlineinit.cpp
+++ b/src/gromacs/commandline/cmdlineinit.cpp
@@ -41,25 +41,24 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/commandline/cmdlineinit.h"
+#include "cmdlineinit.h"
+
+#include "config.h"
 
 #include <cstring>
 
 #include <boost/scoped_ptr.hpp>
 
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-
 #include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/commandline/cmdlineprogramcontext.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/init.h"
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 namespace gmx
 {
 
diff --git a/src/gromacs/commandline/cmdlineinit.h b/src/gromacs/commandline/cmdlineinit.h
index 5c0fc026eb..ae4089f4ae 100644
--- a/src/gromacs/commandline/cmdlineinit.h
+++ b/src/gromacs/commandline/cmdlineinit.h
@@ -47,7 +47,7 @@
 
 // Forward declaration of class CommandLineProgramContext is not sufficient for
 // MSVC if the return value of initForCommandLine() is ignored(!)
-#include "cmdlineprogramcontext.h"
+#include "gromacs/commandline/cmdlineprogramcontext.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/commandline/cmdlinemodulemanager-impl.h b/src/gromacs/commandline/cmdlinemodulemanager-impl.h
index 5a56b68f5c..847b623a75 100644
--- a/src/gromacs/commandline/cmdlinemodulemanager-impl.h
+++ b/src/gromacs/commandline/cmdlinemodulemanager-impl.h
@@ -46,9 +46,8 @@
 #include <string>
 #include <vector>
 
-#include "cmdlinemodule.h"
-#include "cmdlinemodulemanager.h"
-
+#include "gromacs/commandline/cmdlinemodule.h"
+#include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/options/options.h"
 #include "gromacs/utility/common.h"
diff --git a/src/gromacs/commandline/cmdlinemodulemanager.cpp b/src/gromacs/commandline/cmdlinemodulemanager.cpp
index b026f8b0db..8fee8aa10e 100644
--- a/src/gromacs/commandline/cmdlinemodulemanager.cpp
+++ b/src/gromacs/commandline/cmdlinemodulemanager.cpp
@@ -43,26 +43,23 @@
 
 #include "cmdlinemodulemanager.h"
 
+#include "config.h"
+
 #include <cstdio>
 
 #include <string>
 #include <utility>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
 
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/cmdlinehelpmodule.h"
 #include "gromacs/commandline/cmdlineinit.h"
 #include "gromacs/commandline/cmdlinemodule.h"
-#include "gromacs/commandline/cmdlinemodulemanager-impl.h"
 #include "gromacs/commandline/cmdlineparser.h"
 #include "gromacs/commandline/cmdlineprogramcontext.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/utility/basenetwork.h"
@@ -71,6 +68,9 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "cmdlinehelpmodule.h"
+#include "cmdlinemodulemanager-impl.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/commandline/cmdlinemodulemanager.h b/src/gromacs/commandline/cmdlinemodulemanager.h
index 9fb4432f82..62b39488ca 100644
--- a/src/gromacs/commandline/cmdlinemodulemanager.h
+++ b/src/gromacs/commandline/cmdlinemodulemanager.h
@@ -43,9 +43,9 @@
 #ifndef GMX_COMMANDLINE_CMDLINEMODULEMANAGER_H
 #define GMX_COMMANDLINE_CMDLINEMODULEMANAGER_H
 
-#include "../onlinehelp/helptopicinterface.h"
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/uniqueptr.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/commandline/cmdlineparser.h b/src/gromacs/commandline/cmdlineparser.h
index 7f4768c04e..c497410e50 100644
--- a/src/gromacs/commandline/cmdlineparser.h
+++ b/src/gromacs/commandline/cmdlineparser.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -46,7 +46,7 @@
 #include <string>
 #include <vector>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/commandline/cmdlineprogramcontext.h b/src/gromacs/commandline/cmdlineprogramcontext.h
index 206585669a..bfcc17322c 100644
--- a/src/gromacs/commandline/cmdlineprogramcontext.h
+++ b/src/gromacs/commandline/cmdlineprogramcontext.h
@@ -53,8 +53,8 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../utility/common.h"
-#include "../utility/programcontext.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/programcontext.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/commandline/pargs.cpp b/src/gromacs/commandline/pargs.cpp
index 5a16f3cf48..8b7a459d8f 100644
--- a/src/gromacs/commandline/pargs.cpp
+++ b/src/gromacs/commandline/pargs.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/commandline/pargs.h"
+#include "pargs.h"
 
 #include <cstdlib>
 #include <cstring>
diff --git a/src/gromacs/commandline/pargs.h b/src/gromacs/commandline/pargs.h
index f6a2ab680c..9c81a77cb2 100644
--- a/src/gromacs/commandline/pargs.h
+++ b/src/gromacs/commandline/pargs.h
@@ -44,11 +44,11 @@
 #ifndef GMX_COMMANDLINE_PARGS_H
 #define GMX_COMMANDLINE_PARGS_H
 
-#include "../legacyheaders/oenv.h"
-#include "../fileio/filenm.h"
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C"
diff --git a/src/gromacs/commandline/shellcompletions.cpp b/src/gromacs/commandline/shellcompletions.cpp
index e047cf2560..1eefeda1cf 100644
--- a/src/gromacs/commandline/shellcompletions.cpp
+++ b/src/gromacs/commandline/shellcompletions.cpp
@@ -43,7 +43,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/commandline/shellcompletions.h"
+#include "shellcompletions.h"
 
 #include <cstdio>
 
@@ -53,10 +53,10 @@
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"
 #include "gromacs/options/optionsvisitor.h"
-#include "gromacs/fileio/filenm.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
diff --git a/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp b/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
index c5db3a916c..a545dcc835 100644
--- a/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
+++ b/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
@@ -47,10 +47,11 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/commandline/cmdlinehelpwriter.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/cmdlinehelpwriter.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"
diff --git a/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp b/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
index 0d8f4fc4cc..ebb3ee1f5f 100644
--- a/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
+++ b/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
@@ -42,6 +42,8 @@
 // For GMX_BINARY_SUFFIX
 #include "gmxpre.h"
 
+#include "gromacs/commandline/cmdlinemodulemanager.h"
+
 #include "config.h"
 
 #include <vector>
@@ -50,7 +52,6 @@
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
 #include "gromacs/commandline/cmdlinemodule.h"
-#include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/commandline/cmdlineprogramcontext.h"
 #include "gromacs/utility/file.h"
 
diff --git a/src/gromacs/commandline/tests/cmdlineparser.cpp b/src/gromacs/commandline/tests/cmdlineparser.cpp
index 6e408528c5..719e69d34f 100644
--- a/src/gromacs/commandline/tests/cmdlineparser.cpp
+++ b/src/gromacs/commandline/tests/cmdlineparser.cpp
@@ -44,11 +44,12 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/commandline/cmdlineparser.h"
+
 #include <vector>
 
 #include <gtest/gtest.h>
 
-#include "gromacs/commandline/cmdlineparser.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 
diff --git a/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp b/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
index c7ee818a48..f31c3ea405 100644
--- a/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
+++ b/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
@@ -41,20 +41,21 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/commandline/cmdlineprogramcontext.h"
+
+#include "config.h"
+
 #include <string>
 #include <vector>
 
 #include <boost/shared_ptr.hpp>
 #include <gtest/gtest.h>
 
-#include "gromacs/commandline/cmdlineprogramcontext.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/path.h"
 
 #include "testutils/cmdlinetest.h"
 
-#include "config.h"
-
 using gmx::test::CommandLine;
 using gmx::Path;
 
diff --git a/src/gromacs/essentialdynamics/edsam.c b/src/gromacs/essentialdynamics/edsam.c
index 38be02d523..e6cab41f9c 100644
--- a/src/gromacs/essentialdynamics/edsam.c
+++ b/src/gromacs/essentialdynamics/edsam.c
@@ -36,29 +36,29 @@
  */
 #include "gmxpre.h"
 
+#include "edsam.h"
+
 #include <stdio.h>
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/mdlib/groupcoord.h"
-
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 /* We use the same defines as in mvdata.c here */
 #define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d), (cr))
diff --git a/src/gromacs/essentialdynamics/edsam.h b/src/gromacs/essentialdynamics/edsam.h
index 32322ad580..20cbaf442b 100644
--- a/src/gromacs/essentialdynamics/edsam.h
+++ b/src/gromacs/essentialdynamics/edsam.h
@@ -48,8 +48,8 @@
 #ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
 #define GMX_ESSENTIALDYNAMICS_EDSAM_H
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fft/fft.cpp b/src/gromacs/fft/fft.cpp
index 26ac29acbe..2d8a81e17b 100644
--- a/src/gromacs/fft/fft.cpp
+++ b/src/gromacs/fft/fft.cpp
@@ -35,7 +35,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fft/fft.h"
+#include "fft.h"
 
 #include "config.h"
 
diff --git a/src/gromacs/fft/fft.h b/src/gromacs/fft/fft.h
index cfce41baab..69fe46289b 100644
--- a/src/gromacs/fft/fft.h
+++ b/src/gromacs/fft/fft.h
@@ -54,8 +54,8 @@
 
 #include <stdio.h>
 
-#include "../math/gmxcomplex.h"
-#include "../utility/real.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fft/fft5d.cpp b/src/gromacs/fft/fft5d.cpp
index 1e9e11bd70..d226622916 100644
--- a/src/gromacs/fft/fft5d.cpp
+++ b/src/gromacs/fft/fft5d.cpp
@@ -36,6 +36,8 @@
 
 #include "fft5d.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <float.h>
 #include <math.h>
@@ -49,8 +51,6 @@
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 #ifdef NOGMX
 #define GMX_PARALLEL_ENV_INITIALIZED 1
 #else
diff --git a/src/gromacs/fft/fft_fftpack.cpp b/src/gromacs/fft/fft_fftpack.cpp
index c0f412bf6e..1301723da1 100644
--- a/src/gromacs/fft/fft_fftpack.cpp
+++ b/src/gromacs/fft/fft_fftpack.cpp
@@ -35,18 +35,17 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fft/fft.h"
-
 #include <errno.h>
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
+#include "external/fftpack/fftpack.h"
+
+#include "gromacs/fft/fft.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/real.h"
 
-#include "external/fftpack/fftpack.h"
-
 /*! \internal
  * \brief
  * Contents of the FFTPACK fft datatype.
diff --git a/src/gromacs/fft/fft_fftw3.cpp b/src/gromacs/fft/fft_fftw3.cpp
index d83d0f591b..dee2ff284b 100644
--- a/src/gromacs/fft/fft_fftw3.cpp
+++ b/src/gromacs/fft/fft_fftw3.cpp
@@ -35,6 +35,8 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdlib.h>
 
@@ -46,8 +48,6 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
 
-#include "config.h"
-
 #ifdef GMX_DOUBLE
 #define FFTWPREFIX(name) fftw_ ## name
 #else
diff --git a/src/gromacs/fft/parallel_3dfft.cpp b/src/gromacs/fft/parallel_3dfft.cpp
index f721bab65f..3c04fb24fc 100644
--- a/src/gromacs/fft/parallel_3dfft.cpp
+++ b/src/gromacs/fft/parallel_3dfft.cpp
@@ -35,19 +35,18 @@
  */
 #include "gmxpre.h"
 
+#include "parallel_3dfft.h"
+
+#include <errno.h>
 #include <stdlib.h>
 #include <string.h>
-#include <errno.h>
 
 #include "gromacs/fft/fft.h"
-#include "gromacs/fft/parallel_3dfft.h"
+#include "gromacs/fft/fft5d.h"
 #include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
-
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
-
-#include "fft5d.h"
 
 struct gmx_parallel_3dfft  {
     fft5d_plan p1, p2;
diff --git a/src/gromacs/fft/parallel_3dfft.h b/src/gromacs/fft/parallel_3dfft.h
index 2a3fe97d5f..145b0a97b7 100644
--- a/src/gromacs/fft/parallel_3dfft.h
+++ b/src/gromacs/fft/parallel_3dfft.h
@@ -37,13 +37,12 @@
 #ifndef GMX_FFT_PARALLEL_3DFFT_H
 #define GMX_FFT_PARALLEL_3DFFT_H
 
-#include "../math/gmxcomplex.h"
-#include "../timing/wallcycle.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/gmxmpi.h"
-#include "../utility/real.h"
-
-#include "fft.h"
+#include "gromacs/fft/fft.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fft/tests/fft.cpp b/src/gromacs/fft/tests/fft.cpp
index e0d80ad974..446d50307f 100644
--- a/src/gromacs/fft/tests/fft.cpp
+++ b/src/gromacs/fft/tests/fft.cpp
@@ -44,11 +44,12 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/fft/fft.h"
+
 #include <vector>
 
 #include <gtest/gtest.h>
 
-#include "gromacs/fft/fft.h"
 #include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/utility/stringutil.h"
 
diff --git a/src/gromacs/fileio/confio.c b/src/gromacs/fileio/confio.c
index 57aff53965..ef01aa45f7 100644
--- a/src/gromacs/fileio/confio.c
+++ b/src/gromacs/fileio/confio.c
@@ -42,25 +42,24 @@
 #include <math.h>
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
-#include "xdrf.h"
-#include "filenm.h"
-#include "pdbio.h"
-#include "tpxio.h"
-#include "trxio.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gmxfio.h"
-
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define CHAR_SHIFT 24
diff --git a/src/gromacs/fileio/confio.h b/src/gromacs/fileio/confio.h
index 6fbafb3ee4..2b149c23a8 100644
--- a/src/gromacs/fileio/confio.h
+++ b/src/gromacs/fileio/confio.h
@@ -40,9 +40,8 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/simple.h"
-
-#include "trx.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 /* For reading coordinate files it is assumed that enough memory
  * has been allocated beforehand.
diff --git a/src/gromacs/fileio/enxio.c b/src/gromacs/fileio/enxio.c
index d6dce5f4ab..c9b34b1da1 100644
--- a/src/gromacs/fileio/enxio.c
+++ b/src/gromacs/fileio/enxio.c
@@ -41,15 +41,14 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xdrf.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 /* The source code in this file should be thread-safe.
diff --git a/src/gromacs/fileio/enxio.h b/src/gromacs/fileio/enxio.h
index acf41f05f1..c8434ab2b5 100644
--- a/src/gromacs/fileio/enxio.h
+++ b/src/gromacs/fileio/enxio.h
@@ -37,11 +37,11 @@
 #ifndef GMX_FILEIO_ENXIO_H
 #define GMX_FILEIO_ENXIO_H
 
-#include "../legacyheaders/types/energy.h"
-#include "../legacyheaders/types/inputrec.h"
-#include "../legacyheaders/types/state.h"
-#include "gmxfio.h"
-#include "xdr_datatype.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/state.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/filenm.c b/src/gromacs/fileio/filenm.c
index bf8212d2c8..782424df60 100644
--- a/src/gromacs/fileio/filenm.c
+++ b/src/gromacs/fileio/filenm.c
@@ -43,7 +43,6 @@
 
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/fileio/filenm.h b/src/gromacs/fileio/filenm.h
index e4dfab80ae..0dcfd73b9d 100644
--- a/src/gromacs/fileio/filenm.h
+++ b/src/gromacs/fileio/filenm.h
@@ -38,8 +38,8 @@
 #ifndef GMX_FILEIO_FILENM_H
 #define GMX_FILEIO_FILENM_H
 
-#include "../legacyheaders/types/commrec_fwd.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/gmx_system_xdr.c b/src/gromacs/fileio/gmx_system_xdr.c
index cb10ba0abb..9839291218 100644
--- a/src/gromacs/fileio/gmx_system_xdr.c
+++ b/src/gromacs/fileio/gmx_system_xdr.c
@@ -41,12 +41,12 @@
 #ifdef GMX_INTERNAL_XDR
 
 
-#include <stdlib.h>
+#include "gmx_system_xdr.h"
+
 #include <limits.h>
+#include <stdlib.h>
 #include <string.h>
 
-#include "gmx_system_xdr.h"
-
 
 /* NB - THIS FILE IS ONLY USED ON MICROSOFT WINDOWS, since that
  * system doesn't provide any standard XDR system libraries. It will
diff --git a/src/gromacs/fileio/gmxfio.c b/src/gromacs/fileio/gmxfio.c
index e191b217e9..cad0b38951 100644
--- a/src/gromacs/fileio/gmxfio.c
+++ b/src/gromacs/fileio/gmxfio.c
@@ -38,12 +38,12 @@
 
 #include "gmxfio.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
diff --git a/src/gromacs/fileio/gmxfio.h b/src/gromacs/fileio/gmxfio.h
index 8f6401da23..bc656d2ef9 100644
--- a/src/gromacs/fileio/gmxfio.h
+++ b/src/gromacs/fileio/gmxfio.h
@@ -40,10 +40,10 @@
 
 #include <stdio.h>
 
-#include "../utility/cstringutil.h"
-#include "../utility/futil.h"
-#include "../utility/real.h"
-#include "../math/vectypes.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/gmxfio_asc.c b/src/gromacs/fileio/gmxfio_asc.c
index b2f04b7ff8..153e345726 100644
--- a/src/gromacs/fileio/gmxfio_asc.c
+++ b/src/gromacs/fileio/gmxfio_asc.c
@@ -36,13 +36,13 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <ctype.h>
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
diff --git a/src/gromacs/fileio/gmxfio_bin.c b/src/gromacs/fileio/gmxfio_bin.c
index 498a795eb4..9238af5fa1 100644
--- a/src/gromacs/fileio/gmxfio_bin.c
+++ b/src/gromacs/fileio/gmxfio_bin.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
diff --git a/src/gromacs/fileio/gmxfio_int.h b/src/gromacs/fileio/gmxfio_int.h
index cedde9ae90..e7010b15f3 100644
--- a/src/gromacs/fileio/gmxfio_int.h
+++ b/src/gromacs/fileio/gmxfio_int.h
@@ -58,7 +58,7 @@
 
 #include "thread_mpi/lock.h"
 
-#include "xdrf.h"
+#include "gromacs/fileio/xdrf.h"
 
 /* the reader/writer functions  for t_iotype */
 typedef gmx_bool read_func (t_fileio *fio, void *item, int nitem, int eio,
diff --git a/src/gromacs/fileio/gmxfio_rw.c b/src/gromacs/fileio/gmxfio_rw.c
index d41d19176a..bdfa1ec4d8 100644
--- a/src/gromacs/fileio/gmxfio_rw.c
+++ b/src/gromacs/fileio/gmxfio_rw.c
@@ -36,11 +36,11 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdio.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
diff --git a/src/gromacs/fileio/gmxfio_xdr.c b/src/gromacs/fileio/gmxfio_xdr.c
index 6054be42f9..ca1b70d21e 100644
--- a/src/gromacs/fileio/gmxfio_xdr.c
+++ b/src/gromacs/fileio/gmxfio_xdr.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
diff --git a/src/gromacs/fileio/libxdrf.c b/src/gromacs/fileio/libxdrf.c
index 98957275c0..90e58d4ee2 100644
--- a/src/gromacs/fileio/libxdrf.c
+++ b/src/gromacs/fileio/libxdrf.c
@@ -42,8 +42,8 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "xdrf.h"
-#include "xdr_datatype.h"
+#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/fileio/xdrf.h"
 #include "gromacs/utility/futil.h"
 
 /* This is just for clarity - it can never be anything but 4! */
diff --git a/src/gromacs/fileio/matio.h b/src/gromacs/fileio/matio.h
index 988d751d26..1facdf5608 100644
--- a/src/gromacs/fileio/matio.h
+++ b/src/gromacs/fileio/matio.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/rgb.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/legacyheaders/types/rgb.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/md5.c b/src/gromacs/fileio/md5.c
index ad3c36aaad..ff74cc68d0 100644
--- a/src/gromacs/fileio/md5.c
+++ b/src/gromacs/fileio/md5.c
@@ -99,6 +99,7 @@
  */
 
 #include "md5.h"
+
 #include <string.h>
 
 #undef BYTE_ORDER   /* 1 = big-endian, -1 = little-endian, 0 = unknown */
diff --git a/src/gromacs/fileio/mdoutf.c b/src/gromacs/fileio/mdoutf.c
index 4532b7d65b..844c84602e 100644
--- a/src/gromacs/fileio/mdoutf.c
+++ b/src/gromacs/fileio/mdoutf.c
@@ -36,22 +36,21 @@
 
 #include "mdoutf.h"
 
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "trnio.h"
-#include "xtcio.h"
-#include "tngio.h"
-#include "trajectory_writing.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
-
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/mvdata.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/timing/wallcycle.h"
 
 struct gmx_mdoutf {
     t_fileio         *fp_trn;
diff --git a/src/gromacs/fileio/mdoutf.h b/src/gromacs/fileio/mdoutf.h
index 7c9f2a3309..8e241f4e3e 100644
--- a/src/gromacs/fileio/mdoutf.h
+++ b/src/gromacs/fileio/mdoutf.h
@@ -38,15 +38,14 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/inputrec.h"
-#include "../legacyheaders/types/oenv.h"
-#include "../legacyheaders/network.h"
-
-#include "../math/vectypes.h"
-#include "../timing/wallcycle.h"
-#include "../utility/basedefinitions.h"
-#include "filenm.h"
-#include "enxio.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/mtxio.h b/src/gromacs/fileio/mtxio.h
index abbe0fb674..4f9216e5d3 100644
--- a/src/gromacs/fileio/mtxio.h
+++ b/src/gromacs/fileio/mtxio.h
@@ -43,8 +43,8 @@
 #ifndef GMX_FILEIO_MTXIO_H
 #define GMX_FILEIO_MTXIO_H
 
-#include "../linearalgebra/sparsematrix.h"
-#include "../utility/real.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/pdbio.c b/src/gromacs/fileio/pdbio.c
index 05c0cf1322..d5b8a00517 100644
--- a/src/gromacs/fileio/pdbio.c
+++ b/src/gromacs/fileio/pdbio.c
@@ -42,12 +42,10 @@
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/futil.h"
-
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
@@ -57,6 +55,7 @@
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 typedef struct {
diff --git a/src/gromacs/fileio/pdbio.h b/src/gromacs/fileio/pdbio.h
index 241239a8a6..3e13161126 100644
--- a/src/gromacs/fileio/pdbio.h
+++ b/src/gromacs/fileio/pdbio.h
@@ -40,7 +40,7 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/strdb.c b/src/gromacs/fileio/strdb.c
index 21f70b014f..7d6ff971f8 100644
--- a/src/gromacs/fileio/strdb.c
+++ b/src/gromacs/fileio/strdb.c
@@ -42,11 +42,10 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
-
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 gmx_bool get_a_line(FILE *fp, char line[], int n)
 {
diff --git a/src/gromacs/fileio/strdb.h b/src/gromacs/fileio/strdb.h
index bcc2cf98e6..dc35b915ad 100644
--- a/src/gromacs/fileio/strdb.h
+++ b/src/gromacs/fileio/strdb.h
@@ -39,7 +39,7 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/tests/tngio.cpp b/src/gromacs/fileio/tests/tngio.cpp
index 1eab0e4c86..6c5cbef349 100644
--- a/src/gromacs/fileio/tests/tngio.cpp
+++ b/src/gromacs/fileio/tests/tngio.cpp
@@ -41,10 +41,12 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
+#include "gromacs/fileio/tngio.h"
+
 #include <string>
 
-#include "gromacs/fileio/tngio.h"
+#include <gtest/gtest.h>
+
 #include "gromacs/fileio/tngio_for_tools.h"
 #include "gromacs/utility/path.h"
 
diff --git a/src/gromacs/fileio/timecontrol.c b/src/gromacs/fileio/timecontrol.c
index 4c355ae13b..735d649423 100644
--- a/src/gromacs/fileio/timecontrol.c
+++ b/src/gromacs/fileio/timecontrol.c
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fileio/timecontrol.h"
+#include "timecontrol.h"
 
 #include "thread_mpi/threads.h"
 
diff --git a/src/gromacs/fileio/tngio.cpp b/src/gromacs/fileio/tngio.cpp
index b677014564..1303872d3d 100644
--- a/src/gromacs/fileio/tngio.cpp
+++ b/src/gromacs/fileio/tngio.cpp
@@ -46,10 +46,9 @@
 #include "tng/tng_io.h"
 #endif
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
-
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/topology/topology.h"
diff --git a/src/gromacs/fileio/tngio_for_tools.cpp b/src/gromacs/fileio/tngio_for_tools.cpp
index cdc1263bad..b4cfc5f011 100644
--- a/src/gromacs/fileio/tngio_for_tools.cpp
+++ b/src/gromacs/fileio/tngio_for_tools.cpp
@@ -36,10 +36,10 @@
 
 #include "tngio_for_tools.h"
 
-#include <math.h>
-
 #include "config.h"
 
+#include <math.h>
+
 #ifdef GMX_USE_TNG
 #include "tng/tng_io.h"
 #endif
diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.c
index db684d3699..4fba747508 100644
--- a/src/gromacs/fileio/tpxio.c
+++ b/src/gromacs/fileio/tpxio.c
@@ -38,19 +38,18 @@
 
 /* This file is completely threadsafe - keep it that way! */
 
+#include "tpxio.h"
+
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "tpxio.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "confio.h"
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/block.h"
@@ -59,6 +58,7 @@
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define TPX_TAG_RELEASE  "release"
diff --git a/src/gromacs/fileio/tpxio.h b/src/gromacs/fileio/tpxio.h
index 433742fdcd..0b3ca43e31 100644
--- a/src/gromacs/fileio/tpxio.h
+++ b/src/gromacs/fileio/tpxio.h
@@ -47,9 +47,9 @@
  * can also be used with the routines in gmxfio.h
  *
  **************************************************************/
-#include "../legacyheaders/types/inputrec.h"
-#include "../legacyheaders/types/state.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/state.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/trajectory_writing.c b/src/gromacs/fileio/trajectory_writing.c
index c28a834bb5..01b83b7de1 100644
--- a/src/gromacs/fileio/trajectory_writing.c
+++ b/src/gromacs/fileio/trajectory_writing.c
@@ -34,17 +34,17 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "confio.h"
 #include "trajectory_writing.h"
-#include "mdoutf.h"
 
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/smalloc.h"
 
 void
 do_md_trajectory_writing(FILE           *fplog,
diff --git a/src/gromacs/fileio/trajectory_writing.h b/src/gromacs/fileio/trajectory_writing.h
index e604eb58b2..37956342b1 100644
--- a/src/gromacs/fileio/trajectory_writing.h
+++ b/src/gromacs/fileio/trajectory_writing.h
@@ -40,12 +40,11 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/commrec_fwd.h"
-#include "../legacyheaders/mdebin.h"
-#include "../timing/wallcycle.h"
-
-#include "filenm.h"
-#include "mdoutf.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/trnio.c b/src/gromacs/fileio/trnio.c
index a85a82f3c9..a1d6c8cbd7 100644
--- a/src/gromacs/fileio/trnio.c
+++ b/src/gromacs/fileio/trnio.c
@@ -36,14 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "trnio.h"
+
 #include <string.h>
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/txtdump.h"
+
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "trnio.h"
-#include "gmxfio.h"
+#include "gromacs/utility/smalloc.h"
 
 #define BUFSIZE     128
 #define GROMACS_MAGIC   1993
diff --git a/src/gromacs/fileio/trnio.h b/src/gromacs/fileio/trnio.h
index 59bf1d4122..0dcc1e0399 100644
--- a/src/gromacs/fileio/trnio.h
+++ b/src/gromacs/fileio/trnio.h
@@ -53,7 +53,7 @@
  *
  **************************************************************/
 
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/trx.h b/src/gromacs/fileio/trx.h
index dbbfc4b949..9e551b5405 100644
--- a/src/gromacs/fileio/trx.h
+++ b/src/gromacs/fileio/trx.h
@@ -43,9 +43,9 @@
 #ifndef GMX_FILEIO_TRX_H
 #define GMX_FILEIO_TRX_H
 
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/trxio.c b/src/gromacs/fileio/trxio.c
index b6098ce5b3..8e70f73716 100644
--- a/src/gromacs/fileio/trxio.c
+++ b/src/gromacs/fileio/trxio.c
@@ -38,6 +38,8 @@
 
 #include "trxio.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 
@@ -60,8 +62,6 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 #ifdef GMX_USE_PLUGINS
 #include "gromacs/fileio/vmdio.h"
 #endif
diff --git a/src/gromacs/fileio/trxio.h b/src/gromacs/fileio/trxio.h
index f66b4c37f1..0d32e36405 100644
--- a/src/gromacs/fileio/trxio.h
+++ b/src/gromacs/fileio/trxio.h
@@ -38,12 +38,11 @@
 #ifndef GMX_FILEIO_TRXIO_H
 #define GMX_FILEIO_TRXIO_H
 
-#include "../legacyheaders/readinp.h"
-#include "../legacyheaders/oenv.h"
-
-#include "filenm.h"
-#include "gmxfio.h"
-#include "pdbio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/readinp.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/vmdio.c b/src/gromacs/fileio/vmdio.c
index b4ed95239e..621160a9e8 100644
--- a/src/gromacs/fileio/vmdio.c
+++ b/src/gromacs/fileio/vmdio.c
@@ -86,10 +86,10 @@
 /*                                                                           */
 /*****************************************************************************/
 
-#include <stdlib.h>
+#include <assert.h>
 #include <stdio.h>
+#include <stdlib.h>
 #include <string.h>
-#include <assert.h>
 
 /*
  * Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
@@ -102,8 +102,8 @@
 #ifndef _WIN32_IE
 #define _WIN32_IE 0x0500 /* SHGetFolderPath is available since WinXP/IE5 */
 #endif
-#include <windows.h>
 #include <shlobj.h>
+#include <windows.h>
 #endif
 
 #include "gromacs/fileio/gmxfio.h"
diff --git a/src/gromacs/fileio/writeps.c b/src/gromacs/fileio/writeps.c
index cd9d1b407f..a0ae4e15cb 100644
--- a/src/gromacs/fileio/writeps.c
+++ b/src/gromacs/fileio/writeps.c
@@ -40,11 +40,10 @@
 
 #include <stdio.h>
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/smalloc.h"
 
 const char *fontnm[efontNR] = {
     "Times-Roman", "Times-Italic",     "Times-Bold",    "Times-BoldItalic",
diff --git a/src/gromacs/fileio/writeps.h b/src/gromacs/fileio/writeps.h
index 9572efdd9f..33b8dadde2 100644
--- a/src/gromacs/fileio/writeps.h
+++ b/src/gromacs/fileio/writeps.h
@@ -39,9 +39,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/rgb.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/legacyheaders/types/rgb.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/xdrd.c b/src/gromacs/fileio/xdrd.c
index 7edfe5911a..5af573e7b3 100644
--- a/src/gromacs/fileio/xdrd.c
+++ b/src/gromacs/fileio/xdrd.c
@@ -36,8 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "xdrf.h"
-
+#include "gromacs/fileio/xdrf.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/fileio/xdrf.h b/src/gromacs/fileio/xdrf.h
index 5563c58e86..dd2959e986 100644
--- a/src/gromacs/fileio/xdrf.h
+++ b/src/gromacs/fileio/xdrf.h
@@ -49,7 +49,7 @@
 #include "config.h"
 
 #ifdef GMX_INTERNAL_XDR
-#include "gmx_system_xdr.h"
+#include "gromacs/fileio/gmx_system_xdr.h"
 #else
 #include <rpc/rpc.h>
 #include <rpc/xdr.h>
diff --git a/src/gromacs/fileio/xtcio.h b/src/gromacs/fileio/xtcio.h
index 18ebc044c9..2c50fb89f0 100644
--- a/src/gromacs/fileio/xtcio.h
+++ b/src/gromacs/fileio/xtcio.h
@@ -38,10 +38,10 @@
 #ifndef GMX_FILEIO_XTCIO_H
 #define GMX_FILEIO_XTCIO_H
 
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/fileio/xvgr.cpp b/src/gromacs/fileio/xvgr.cpp
index dddebce5a1..fc65cf8d02 100644
--- a/src/gromacs/fileio/xvgr.cpp
+++ b/src/gromacs/fileio/xvgr.cpp
@@ -36,22 +36,21 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/fileio/xvgr.h"
+#include "xvgr.h"
 
 #include "config.h"
 
-#include <string.h>
 #include <ctype.h>
+#include <string.h>
 #include <time.h>
 
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
 
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/oenv.h"
-
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
diff --git a/src/gromacs/fileio/xvgr.h b/src/gromacs/fileio/xvgr.h
index 8aa6c35cc7..542387b189 100644
--- a/src/gromacs/fileio/xvgr.h
+++ b/src/gromacs/fileio/xvgr.h
@@ -39,9 +39,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/oenv.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxana/anadih.c b/src/gromacs/gmxana/anadih.c
index a73525d676..c967c601c8 100644
--- a/src/gromacs/gmxana/anadih.c
+++ b/src/gromacs/gmxana/anadih.c
@@ -39,20 +39,20 @@
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
-#include "gromacs/math/units.h"
-#include "gromacs/utility/smalloc.h"
+
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gstat.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/bonded/bonded.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 void print_one(const output_env_t oenv, const char *base, const char *name,
                const char *title, const char *ylabel, int nf, real time[],
diff --git a/src/gromacs/gmxana/autocorr.c b/src/gromacs/gmxana/autocorr.c
index 5e829a986d..9b0a13b691 100644
--- a/src/gromacs/gmxana/autocorr.c
+++ b/src/gromacs/gmxana/autocorr.c
@@ -40,16 +40,16 @@
 #include <stdio.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "correl.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define MODE(x) ((mode & (x)) == (x))
 
diff --git a/src/gromacs/gmxana/cmat.c b/src/gromacs/gmxana/cmat.c
index fab169f798..672a2b60b2 100644
--- a/src/gromacs/gmxana/cmat.c
+++ b/src/gromacs/gmxana/cmat.c
@@ -37,12 +37,13 @@
 #include "gmxpre.h"
 
 #include "cmat.h"
-#include "gromacs/utility/smalloc.h"
+
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/fileio/matio.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 t_mat *init_mat(int n1, gmx_bool b1D)
 {
diff --git a/src/gromacs/gmxana/correl.c b/src/gromacs/gmxana/correl.c
index b223ad0adb..a8c8c430ff 100644
--- a/src/gromacs/gmxana/correl.c
+++ b/src/gromacs/gmxana/correl.c
@@ -37,13 +37,14 @@
 
 #include "gmxpre.h"
 
+#include "correl.h"
+
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <math.h>
 
 #include "gromacs/fft/fft.h"
 #include "gromacs/utility/smalloc.h"
-#include "correl.h"
 
 #define SWAP(a, b) tempr = (a); (a) = (b); (b) = tempr
 
diff --git a/src/gromacs/gmxana/correl.h b/src/gromacs/gmxana/correl.h
index bdc8f5078d..5851d6c28c 100644
--- a/src/gromacs/gmxana/correl.h
+++ b/src/gromacs/gmxana/correl.h
@@ -39,8 +39,8 @@
 #ifndef _correl_h
 #define _correl_h
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fft/fft.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 typedef struct {
     int        n;
diff --git a/src/gromacs/gmxana/dens_filter.c b/src/gromacs/gmxana/dens_filter.c
index 0bf0bfc7d2..bd08b5247a 100644
--- a/src/gromacs/gmxana/dens_filter.c
+++ b/src/gromacs/gmxana/dens_filter.c
@@ -39,11 +39,13 @@
  * Routines for Filters and convolutions
  */
 
+#include "dens_filter.h"
+
 #include <math.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
-#include "dens_filter.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_DOUBLE
 #define EXP(x) (exp(x))
diff --git a/src/gromacs/gmxana/dlist.c b/src/gromacs/gmxana/dlist.c
index d1e1d27a3b..b7578cef62 100644
--- a/src/gromacs/gmxana/dlist.c
+++ b/src/gromacs/gmxana/dlist.c
@@ -39,8 +39,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gstat.h"
-
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/gmxana/edittop.c b/src/gromacs/gmxana/edittop.c
index 9902937ced..3a5357c731 100644
--- a/src/gromacs/gmxana/edittop.c
+++ b/src/gromacs/gmxana/edittop.c
@@ -38,8 +38,8 @@
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/symtab.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 void replace_atom(t_topology *top, int inr, char *anm, char *resnm,
                   real q, real m, int type)
diff --git a/src/gromacs/gmxana/eigio.c b/src/gromacs/gmxana/eigio.c
index b645b777ca..8d65ffbc59 100644
--- a/src/gromacs/gmxana/eigio.c
+++ b/src/gromacs/gmxana/eigio.c
@@ -36,12 +36,13 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
 #include "eigio.h"
-#include "gromacs/fileio/trnio.h"
+
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 void read_eigenvectors(const char *file, int *natoms, gmx_bool *bFit,
                        rvec **xref, gmx_bool *bDMR,
diff --git a/src/gromacs/gmxana/expfit.c b/src/gromacs/gmxana/expfit.c
index b9d57723a1..61f9f7699e 100644
--- a/src/gromacs/gmxana/expfit.c
+++ b/src/gromacs/gmxana/expfit.c
@@ -39,14 +39,13 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 const int   nfp_ffn[effnNR] = { 0, 1, 2, 3, 2, 5, 7, 9, 4, 3};
 
diff --git a/src/gromacs/gmxana/fitahx.c b/src/gromacs/gmxana/fitahx.c
index 0281600229..24b5a955d1 100644
--- a/src/gromacs/gmxana/fitahx.c
+++ b/src/gromacs/gmxana/fitahx.c
@@ -37,9 +37,9 @@
 #include "gmxpre.h"
 
 #include "fitahx.h"
-#include "gromacs/math/vec.h"
 
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxana/fitahx.h b/src/gromacs/gmxana/fitahx.h
index 01d1c7c3de..399028ef05 100644
--- a/src/gromacs/gmxana/fitahx.h
+++ b/src/gromacs/gmxana/fitahx.h
@@ -39,8 +39,8 @@
 #define _fitahx_h
 
 
+#include "gromacs/gmxana/hxprops.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "hxprops.h"
 
 extern real fit_ahx(int nres, t_bb bb[], int natoms, int nall, atom_id allindex[],
                     rvec x[], int nca, atom_id caindex[], gmx_bool bFit);
diff --git a/src/gromacs/gmxana/geminate.c b/src/gromacs/gmxana/geminate.c
index 273f7ae92a..2b8603dfe6 100644
--- a/src/gromacs/gmxana/geminate.c
+++ b/src/gromacs/gmxana/geminate.c
@@ -34,16 +34,16 @@
  */
 #include "gmxpre.h"
 
+#include "geminate.h"
+
 #include <math.h>
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
-#include "geminate.h"
-
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
 
 static void missing_code_message()
 {
diff --git a/src/gromacs/gmxana/gmx_anadock.c b/src/gromacs/gmxana/gmx_anadock.c
index b0e506085c..98675b5687 100644
--- a/src/gromacs/gmxana/gmx_anadock.c
+++ b/src/gromacs/gmxana/gmx_anadock.c
@@ -39,18 +39,18 @@
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/statistics/statistics.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static const char *etitles[] = { "E-docked", "Free Energy" };
 
diff --git a/src/gromacs/gmxana/gmx_anaeig.c b/src/gromacs/gmxana/gmx_anaeig.c
index dde9815f2a..4a219adf2c 100644
--- a/src/gromacs/gmxana/gmx_anaeig.c
+++ b/src/gromacs/gmxana/gmx_anaeig.c
@@ -41,27 +41,26 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "eigio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void calc_entropy_qh(FILE *fp, int n, real eigval[], real temp, int nskip)
 {
diff --git a/src/gromacs/gmxana/gmx_analyze.c b/src/gromacs/gmxana/gmx_analyze.c
index 94400867e5..a2f9799621 100644
--- a/src/gromacs/gmxana/gmx_analyze.c
+++ b/src/gromacs/gmxana/gmx_analyze.c
@@ -41,23 +41,22 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gstat.h"
-#include "gromacs/statistics/statistics.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-#include "geminate.h"
-
 #include "gromacs/linearalgebra/matrix.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* must correspond to char *avbar_opt[] declared in main() */
 enum {
diff --git a/src/gromacs/gmxana/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c
index 8064d062f1..2a093478e4 100644
--- a/src/gromacs/gmxana/gmx_angle.c
+++ b/src/gromacs/gmxana/gmx_angle.c
@@ -39,21 +39,21 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
-#include "gromacs/fileio/trnio.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void dump_dih_trn(int nframes, int nangles, real **dih, const char *fn,
diff --git a/src/gromacs/gmxana/gmx_bar.c b/src/gromacs/gmxana/gmx_bar.c
index e366081d07..2a2b8fd8cb 100644
--- a/src/gromacs/gmxana/gmx_bar.c
+++ b/src/gromacs/gmxana/gmx_bar.c
@@ -40,21 +40,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/enxio.h"
-#include "gromacs/math/units.h"
-#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* Structure for the names of lambda vector components */
diff --git a/src/gromacs/gmxana/gmx_bundle.c b/src/gromacs/gmxana/gmx_bundle.c
index d98f7d600e..4b55d0d406 100644
--- a/src/gromacs/gmxana/gmx_bundle.c
+++ b/src/gromacs/gmxana/gmx_bundle.c
@@ -40,20 +40,19 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gmx_ana.h"
-
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define MAX_ENDS 3
 
diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index 0c5a02a21c..8c377df06a 100644
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -40,25 +40,25 @@
 #include <stdio.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
-#include "gromacs/topology/residuetypes.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static gmx_bool bAllowed(real phi, real psi)
 {
diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
index d1984d58e5..e93a10f95e 100644
--- a/src/gromacs/gmxana/gmx_cluster.c
+++ b/src/gromacs/gmxana/gmx_cluster.c
@@ -40,30 +40,28 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/random/random.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "cmat.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* print to two file pointers at once (i.e. stderr and log) */
 static gmx_inline
diff --git a/src/gromacs/gmxana/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
index 3800dceca9..2f9d219d7d 100644
--- a/src/gromacs/gmxana/gmx_clustsize.c
+++ b/src/gromacs/gmxana/gmx_clustsize.c
@@ -38,27 +38,26 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/math/units.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/pme.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gmx_ana.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void clust_size(const char *ndx, const char *trx, const char *xpm,
                        const char *xpmw, const char *ncl, const char *acl,
diff --git a/src/gromacs/gmxana/gmx_confrms.c b/src/gromacs/gmxana/gmx_confrms.c
index 8923544657..3cc6dc6d14 100644
--- a/src/gromacs/gmxana/gmx_confrms.c
+++ b/src/gromacs/gmxana/gmx_confrms.c
@@ -39,24 +39,23 @@
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/filenm.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
-
-#include "gromacs/math/do_fit.h"
+#include "gromacs/utility/smalloc.h"
 
 void calc_rm_cm(int isize, atom_id index[], t_atoms *atoms, rvec x[], rvec xcm)
 {
diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
index 59411cd549..57756726ed 100644
--- a/src/gromacs/gmxana/gmx_covar.c
+++ b/src/gromacs/gmxana/gmx_covar.c
@@ -47,26 +47,25 @@
 #endif
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/matio.h"
-#include "eigio.h"
-#include "gmx_ana.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/trxio.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_covar(int argc, char *argv[])
 {
diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index 42d316bb2e..e27cf05233 100644
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -38,21 +38,20 @@
 #include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/statistics/statistics.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #define SQR(x) (pow(x, 2.0))
 #define EPSI0 (EPSILON0*E_CHARGE*E_CHARGE*AVOGADRO/(KILO*NANO)) /* EPSILON0 in SI units */
diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index 43a3180d67..f74611b940 100644
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -41,23 +41,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/gmxana/gmx_densmap.c b/src/gromacs/gmxana/gmx_densmap.c
index a71c04137f..03bc88dd11 100644
--- a/src/gromacs/gmxana/gmx_densmap.c
+++ b/src/gromacs/gmxana/gmx_densmap.c
@@ -40,22 +40,21 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_densmap(int argc, char *argv[])
 {
diff --git a/src/gromacs/gmxana/gmx_densorder.cpp b/src/gromacs/gmxana/gmx_densorder.cpp
index 5d8a8d9bb1..99f6807992 100644
--- a/src/gromacs/gmxana/gmx_densorder.cpp
+++ b/src/gromacs/gmxana/gmx_densorder.cpp
@@ -38,29 +38,28 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/math/units.h"
-#include "dens_filter.h"
-#include "binsearch.h"
-#include "powerspect.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/binsearch.h"
+#include "gromacs/gmxana/dens_filter.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/powerspect.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_DOUBLE
diff --git a/src/gromacs/gmxana/gmx_dielectric.c b/src/gromacs/gmxana/gmx_dielectric.c
index e9c6445dd6..5f4ce88446 100644
--- a/src/gromacs/gmxana/gmx_dielectric.c
+++ b/src/gromacs/gmxana/gmx_dielectric.c
@@ -40,20 +40,19 @@
 #include <stdio.h>
 #include <stdlib.h>
 
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gstat.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "gromacs/utility/fatalerror.h"
-
-#include "gromacs/utility/futil.h"
 #include "gromacs/math/gmxcomplex.h"
 #include "gromacs/math/utilities.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Determines at which point in the array the fit should start */
 int calc_nbegin(int nx, real x[], real tbegin)
diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index 68e338fe04..b930a6115e 100644
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -36,37 +36,36 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
 #include <math.h>
+#include <string.h>
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/statistics/statistics.h"
-#include "gstat.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/random/random.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/calcmu.h"
-#include "gromacs/fileio/enxio.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/fileio/trxio.h"
-
 #include "gromacs/bonded/bonded.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define e2d(x) ENM2DEBYE*(x)
diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index d7e1dd8af8..e6d0f29854 100644
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -40,34 +40,33 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gstat.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxana/gmx_do_dssp.c b/src/gromacs/gmxana/gmx_do_dssp.c
index 45e7a87663..610f52a10e 100644
--- a/src/gromacs/gmxana/gmx_do_dssp.c
+++ b/src/gromacs/gmxana/gmx_do_dssp.c
@@ -40,20 +40,19 @@
 
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/topology/index.h"
-#include "gstat.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/viewit.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index 07439151bc..65b6eaad3d 100644
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -39,25 +39,25 @@
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fft/fft.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 enum {
     VACF, MVACF, DOS, DOS_SOLID, DOS_DIFF, DOS_CP, DOS_S, DOS_A, DOS_E, DOS_NR
diff --git a/src/gromacs/gmxana/gmx_dyecoupl.c b/src/gromacs/gmxana/gmx_dyecoupl.c
index 424c73842e..57f2e47dca 100644
--- a/src/gromacs/gmxana/gmx_dyecoupl.c
+++ b/src/gromacs/gmxana/gmx_dyecoupl.c
@@ -34,15 +34,14 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/gmxana/gmx_dyndom.c b/src/gromacs/gmxana/gmx_dyndom.c
index 7b2ac8e499..5a727cb1c2 100644
--- a/src/gromacs/gmxana/gmx_dyndom.c
+++ b/src/gromacs/gmxana/gmx_dyndom.c
@@ -36,17 +36,16 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/atoms.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxana/gmx_editconf.c b/src/gromacs/gmxana/gmx_editconf.c
index abe79cb071..02069c9945 100644
--- a/src/gromacs/gmxana/gmx_editconf.c
+++ b/src/gromacs/gmxana/gmx_editconf.c
@@ -39,26 +39,25 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/fileio/pdbio.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "gromacs/math/units.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "princ.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxana/gmx_eneconv.c b/src/gromacs/gmxana/gmx_eneconv.c
index 34dea59357..9a1e775ef6 100644
--- a/src/gromacs/gmxana/gmx_eneconv.c
+++ b/src/gromacs/gmxana/gmx_eneconv.c
@@ -40,17 +40,17 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #define TIME_EXPLICIT 0
 #define TIME_CONTINUE 1
diff --git a/src/gromacs/gmxana/gmx_enemat.c b/src/gromacs/gmxana/gmx_enemat.c
index bae15a8ae0..576cb221eb 100644
--- a/src/gromacs/gmxana/gmx_enemat.c
+++ b/src/gromacs/gmxana/gmx_enemat.c
@@ -36,25 +36,25 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
 #include <math.h>
+#include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gstat.h"
-#include "gromacs/math/units.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/strdb.h"
-#include "gmx_ana.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static int search_str2(int nstr, char **str, char *key)
diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index 96a153cf0c..3319c96e81 100644
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -40,25 +40,25 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gstat.h"
-#include "gromacs/math/units.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static real       minthird = -1.0/3.0, minsixth = -1.0/6.0;
 
diff --git a/src/gromacs/gmxana/gmx_filter.c b/src/gromacs/gmxana/gmx_filter.c
index 4b1909c8a3..cb26f11be0 100644
--- a/src/gromacs/gmxana/gmx_filter.c
+++ b/src/gromacs/gmxana/gmx_filter.c
@@ -40,18 +40,17 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_filter(int argc, char *argv[])
 {
diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index 1301d8e01a..befd4b4bbc 100644
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -40,22 +40,22 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/confio.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/math/utilities.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/tpxio.h"
 #include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
 #include "gromacs/topology/index.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void insert_ion(int nsa, int *nwater,
                        gmx_bool bSet[], int repl[], atom_id index[],
diff --git a/src/gromacs/gmxana/gmx_genpr.c b/src/gromacs/gmxana/gmx_genpr.c
index a883f697a8..1dbe1e35e5 100644
--- a/src/gromacs/gmxana/gmx_genpr.c
+++ b/src/gromacs/gmxana/gmx_genpr.c
@@ -40,16 +40,16 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_genpr(int argc, char *argv[])
 {
diff --git a/src/gromacs/gmxana/gmx_gyrate.c b/src/gromacs/gmxana/gmx_gyrate.c
index f8bb1f3758..a1f3622fdc 100644
--- a/src/gromacs/gmxana/gmx_gyrate.c
+++ b/src/gromacs/gmxana/gmx_gyrate.c
@@ -40,23 +40,22 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "princ.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gstat.h"
-#include "gmx_ana.h"
-
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 real calc_gyro(rvec x[], int gnx, atom_id index[], t_atom atom[], real tm,
                rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)
diff --git a/src/gromacs/gmxana/gmx_h2order.c b/src/gromacs/gmxana/gmx_h2order.c
index 27e918b8d3..284ca5517b 100644
--- a/src/gromacs/gmxana/gmx_h2order.c
+++ b/src/gromacs/gmxana/gmx_h2order.c
@@ -39,21 +39,20 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/index.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /****************************************************************************/
 /* This program calculates the ordering of water molecules across a box, as */
diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index 46a4da6497..06911ed582 100644
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <math.h>
 
 #include "gromacs/commandline/pargs.h"
@@ -61,8 +63,6 @@
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 /*#define HAVE_NN_LOOPS*/
 
 typedef short int t_E;
diff --git a/src/gromacs/gmxana/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
index b1bbcb8d6d..3d18d53f3c 100644
--- a/src/gromacs/gmxana/gmx_helix.c
+++ b/src/gromacs/gmxana/gmx_helix.c
@@ -39,26 +39,25 @@
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "fitahx.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
-#include "hxprops.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/fitahx.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/hxprops.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_helix(int argc, char *argv[])
 {
diff --git a/src/gromacs/gmxana/gmx_helixorient.c b/src/gromacs/gmxana/gmx_helixorient.c
index dfd3a1f7cf..7946fd306f 100644
--- a/src/gromacs/gmxana/gmx_helixorient.c
+++ b/src/gromacs/gmxana/gmx_helixorient.c
@@ -38,19 +38,18 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
-#include "gstat.h"
-#include "gmx_ana.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/gmxana/gmx_hydorder.c b/src/gromacs/gmxana/gmx_hydorder.c
index 74de61fc81..37038b0af4 100644
--- a/src/gromacs/gmxana/gmx_hydorder.c
+++ b/src/gromacs/gmxana/gmx_hydorder.c
@@ -38,23 +38,22 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "binsearch.h"
-#include "powerspect.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/binsearch.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/powerspect.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 /* Print name of first atom in all groups in index file */
diff --git a/src/gromacs/gmxana/gmx_lie.c b/src/gromacs/gmxana/gmx_lie.c
index 250256d475..f6ab7c1033 100644
--- a/src/gromacs/gmxana/gmx_lie.c
+++ b/src/gromacs/gmxana/gmx_lie.c
@@ -42,18 +42,18 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/fileio/enxio.h"
-#include "gstat.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     int  nlj, nqq;
diff --git a/src/gromacs/gmxana/gmx_make_edi.c b/src/gromacs/gmxana/gmx_make_edi.c
index 7c1ec8411c..9665117ac1 100644
--- a/src/gromacs/gmxana/gmx_make_edi.c
+++ b/src/gromacs/gmxana/gmx_make_edi.c
@@ -38,26 +38,27 @@
  */
 #include "gmxpre.h"
 
+#include <ctype.h>
 #include <math.h>
 #include <stdlib.h>
-#include <ctype.h>
 #include <string.h>
-#include "gromacs/legacyheaders/readinp.h"
+
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "eigio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct
 {
diff --git a/src/gromacs/gmxana/gmx_make_ndx.c b/src/gromacs/gmxana/gmx_make_ndx.c
index be16251aef..55dc3ab47b 100644
--- a/src/gromacs/gmxana/gmx_make_ndx.c
+++ b/src/gromacs/gmxana/gmx_make_ndx.c
@@ -39,17 +39,16 @@
 #include <ctype.h>
 #include <string.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/math/vec.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 /* It's not nice to have size limits, but we should not spend more time
diff --git a/src/gromacs/gmxana/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.c
index cc0a6e2bec..960049e5cf 100644
--- a/src/gromacs/gmxana/gmx_mdmat.c
+++ b/src/gromacs/gmxana/gmx_mdmat.c
@@ -39,22 +39,22 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/filenm.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gmx_ana.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 #define FARAWAY 10000
diff --git a/src/gromacs/gmxana/gmx_mindist.c b/src/gromacs/gmxana/gmx_mindist.c
index 3b732ffe0a..920f6cc3a7 100644
--- a/src/gromacs/gmxana/gmx_mindist.c
+++ b/src/gromacs/gmxana/gmx_mindist.c
@@ -40,21 +40,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void periodic_dist(int ePBC,
diff --git a/src/gromacs/gmxana/gmx_mk_angndx.c b/src/gromacs/gmxana/gmx_mk_angndx.c
index d27546891a..21af93c9b0 100644
--- a/src/gromacs/gmxana/gmx_mk_angndx.c
+++ b/src/gromacs/gmxana/gmx_mk_angndx.c
@@ -37,13 +37,14 @@
 #include "gmxpre.h"
 
 #include <math.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static int calc_ntype(int nft, int *ft, t_idef *idef)
 {
diff --git a/src/gromacs/gmxana/gmx_morph.c b/src/gromacs/gmxana/gmx_morph.c
index 8e77699e89..fe1153db71 100644
--- a/src/gromacs/gmxana/gmx_morph.c
+++ b/src/gromacs/gmxana/gmx_morph.c
@@ -36,17 +36,16 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/topology/index.h"
-#include "gmx_ana.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/topology/atoms.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxana/gmx_msd.c b/src/gromacs/gmxana/gmx_msd.c
index 701f412114..6913929759 100644
--- a/src/gromacs/gmxana/gmx_msd.c
+++ b/src/gromacs/gmxana/gmx_msd.c
@@ -39,24 +39,23 @@
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
-#include "gromacs/statistics/statistics.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define FACTOR  1000.0  /* Convert nm^2/ps to 10e-5 cm^2/s */
diff --git a/src/gromacs/gmxana/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
index 519f44a3bf..eb727c8fa2 100644
--- a/src/gromacs/gmxana/gmx_nmeig.c
+++ b/src/gromacs/gmxana/gmx_nmeig.c
@@ -39,23 +39,22 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "eigio.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/mtxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static double cv_corr(double nu, double T)
diff --git a/src/gromacs/gmxana/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.c
index a734478f8d..0d005fe5cd 100644
--- a/src/gromacs/gmxana/gmx_nmens.c
+++ b/src/gromacs/gmxana/gmx_nmens.c
@@ -40,21 +40,21 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
-#include "eigio.h"
-#include "gmx_ana.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 int gmx_nmens(int argc, char *argv[])
diff --git a/src/gromacs/gmxana/gmx_nmtraj.c b/src/gromacs/gmxana/gmx_nmtraj.c
index 661caf2749..2fbe5cdb1f 100644
--- a/src/gromacs/gmxana/gmx_nmtraj.c
+++ b/src/gromacs/gmxana/gmx_nmtraj.c
@@ -41,19 +41,19 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "eigio.h"
-#include "gmx_ana.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 int gmx_nmtraj(int argc, char *argv[])
diff --git a/src/gromacs/gmxana/gmx_options.c b/src/gromacs/gmxana/gmx_options.c
index addcdc5f4b..52b99ead39 100644
--- a/src/gromacs/gmxana/gmx_options.c
+++ b/src/gromacs/gmxana/gmx_options.c
@@ -36,9 +36,9 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 /*
  * This program is needed to create the files:
diff --git a/src/gromacs/gmxana/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
index 7c2b600d05..28c3e77722 100644
--- a/src/gromacs/gmxana/gmx_order.c
+++ b/src/gromacs/gmxana/gmx_order.c
@@ -39,24 +39,23 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/confio.h"
-#include "cmat.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 /****************************************************************************/
diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 0dc23d9f85..0b0373833e 100644
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -34,31 +34,30 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/calcgrid.h"
 #include "gromacs/legacyheaders/checkpoint.h"
-#include "gmx_ana.h"
-#include "gromacs/random/random.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
-
-#include "config.h"
+#include "gromacs/utility/smalloc.h"
 
 /* We use the same defines as in mvdata.c here */
 #define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d), (cr))
diff --git a/src/gromacs/gmxana/gmx_polystat.c b/src/gromacs/gmxana/gmx_polystat.c
index 367c1c5ff6..ece18dc4d1 100644
--- a/src/gromacs/gmxana/gmx_polystat.c
+++ b/src/gromacs/gmxana/gmx_polystat.c
@@ -39,21 +39,20 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void gyro_eigen(double **gyr, double *eig, double **eigv, int *ord)
 {
diff --git a/src/gromacs/gmxana/gmx_potential.c b/src/gromacs/gmxana/gmx_potential.c
index ba223b01cc..9991682a45 100644
--- a/src/gromacs/gmxana/gmx_potential.c
+++ b/src/gromacs/gmxana/gmx_potential.c
@@ -40,22 +40,21 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/topology/index.h"
-#include "gmx_ana.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/trxio.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define EPS0 8.85419E-12
 #define ELC 1.60219E-19
diff --git a/src/gromacs/gmxana/gmx_principal.c b/src/gromacs/gmxana/gmx_principal.c
index 5be044744a..9780027dd6 100644
--- a/src/gromacs/gmxana/gmx_principal.c
+++ b/src/gromacs/gmxana/gmx_principal.c
@@ -40,20 +40,20 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gstat.h"
-#include "gmx_ana.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 void
diff --git a/src/gromacs/gmxana/gmx_rama.c b/src/gromacs/gmxana/gmx_rama.c
index 711bac7ece..5198b0c730 100644
--- a/src/gromacs/gmxana/gmx_rama.c
+++ b/src/gromacs/gmxana/gmx_rama.c
@@ -39,17 +39,17 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/nrama.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/commandline/pargs.h"
-#include "nrama.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void plot_rama(FILE *out, t_xrama *xr)
diff --git a/src/gromacs/gmxana/gmx_rdf.c b/src/gromacs/gmxana/gmx_rdf.c
index db06a91279..47c4bc0c6f 100644
--- a/src/gromacs/gmxana/gmx_rdf.c
+++ b/src/gromacs/gmxana/gmx_rdf.c
@@ -39,25 +39,24 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/coulomb.h"
-#include "gstat.h"
-#include "gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static void check_box_c(matrix box)
diff --git a/src/gromacs/gmxana/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
index 24af686324..dccad9e472 100644
--- a/src/gromacs/gmxana/gmx_rms.c
+++ b/src/gromacs/gmxana/gmx_rms.c
@@ -39,26 +39,25 @@
 #include <math.h>
 #include <stdlib.h>
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "cmat.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void norm_princ(t_atoms *atoms, int isize, atom_id *index, int natoms,
                        rvec *x)
diff --git a/src/gromacs/gmxana/gmx_rmsdist.c b/src/gromacs/gmxana/gmx_rmsdist.c
index 504ba2abc2..ea98add60a 100644
--- a/src/gromacs/gmxana/gmx_rmsdist.c
+++ b/src/gromacs/gmxana/gmx_rmsdist.c
@@ -38,23 +38,22 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/strdb.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/strdb.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void calc_dist(int nind, atom_id index[], rvec x[], int ePBC, matrix box,
diff --git a/src/gromacs/gmxana/gmx_rmsf.c b/src/gromacs/gmxana/gmx_rmsf.c
index de56950586..c4398533cd 100644
--- a/src/gromacs/gmxana/gmx_rmsf.c
+++ b/src/gromacs/gmxana/gmx_rmsf.c
@@ -38,25 +38,24 @@
 
 #include <math.h>
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/utility/futil.h"
-#include "princ.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static real find_pdb_bfac(t_atoms *atoms, t_resinfo *ri, char *atomnm)
 {
diff --git a/src/gromacs/gmxana/gmx_rotacf.c b/src/gromacs/gmxana/gmx_rotacf.c
index 0895c01bb2..4eb9a6ec18 100644
--- a/src/gromacs/gmxana/gmx_rotacf.c
+++ b/src/gromacs/gmxana/gmx_rotacf.c
@@ -39,19 +39,18 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 int gmx_rotacf(int argc, char *argv[])
diff --git a/src/gromacs/gmxana/gmx_rotmat.c b/src/gromacs/gmxana/gmx_rotmat.c
index e4606039b4..3eddfe424c 100644
--- a/src/gromacs/gmxana/gmx_rotmat.c
+++ b/src/gromacs/gmxana/gmx_rotmat.c
@@ -38,20 +38,19 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void get_refx(output_env_t oenv, const char *trxfn, int nfitdim, int skip,
                      int gnx, int *index,
diff --git a/src/gromacs/gmxana/gmx_saltbr.c b/src/gromacs/gmxana/gmx_saltbr.c
index 47b3e6cca7..46fd1409e1 100644
--- a/src/gromacs/gmxana/gmx_saltbr.c
+++ b/src/gromacs/gmxana/gmx_saltbr.c
@@ -39,20 +39,18 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     char *label;
diff --git a/src/gromacs/gmxana/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
index a91af5888b..797652dd8d 100644
--- a/src/gromacs/gmxana/gmx_sans.c
+++ b/src/gromacs/gmxana/gmx_sans.c
@@ -37,20 +37,19 @@
 
 #include "config.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/topology/index.h"
-#include "gstat.h"
-#include "gmx_ana.h"
-#include "nsfactor.h"
-
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/nsfactor.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxomp.h"
diff --git a/src/gromacs/gmxana/gmx_saxs.c b/src/gromacs/gmxana/gmx_saxs.c
index 73ab9694db..30967feab7 100644
--- a/src/gromacs/gmxana/gmx_saxs.c
+++ b/src/gromacs/gmxana/gmx_saxs.c
@@ -39,12 +39,11 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gmx_ana.h"
-#include "sfactor.h"
-
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/sfactor.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/smalloc.h"
 
 int gmx_saxs(int argc, char *argv[])
diff --git a/src/gromacs/gmxana/gmx_sham.c b/src/gromacs/gmxana/gmx_sham.c
index c2a0ae7423..863e820489 100644
--- a/src/gromacs/gmxana/gmx_sham.c
+++ b/src/gromacs/gmxana/gmx_sham.c
@@ -41,20 +41,20 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gstat.h"
-#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static int index2(int *ibox, int x, int y)
diff --git a/src/gromacs/gmxana/gmx_sigeps.c b/src/gromacs/gmxana/gmx_sigeps.c
index a4860c8d70..4eaae62fb6 100644
--- a/src/gromacs/gmxana/gmx_sigeps.c
+++ b/src/gromacs/gmxana/gmx_sigeps.c
@@ -39,19 +39,19 @@
 #include <math.h>
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
 
 real pot(real x, real qq, real c6, real cn, int npow)
 {
diff --git a/src/gromacs/gmxana/gmx_sorient.c b/src/gromacs/gmxana/gmx_sorient.c
index 5c37813228..a81a8265d5 100644
--- a/src/gromacs/gmxana/gmx_sorient.c
+++ b/src/gromacs/gmxana/gmx_sorient.c
@@ -36,19 +36,18 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxana/gmx_spatial.c b/src/gromacs/gmxana/gmx_spatial.c
index 4eb86003d4..600608d2e3 100644
--- a/src/gromacs/gmxana/gmx_spatial.c
+++ b/src/gromacs/gmxana/gmx_spatial.c
@@ -38,16 +38,16 @@
 #include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
 
 static const double bohr = 0.529177249;  /* conversion factor to compensate for VMD plugin conversion... */
 
diff --git a/src/gromacs/gmxana/gmx_spol.c b/src/gromacs/gmxana/gmx_spol.c
index e715f578c3..2def7422e5 100644
--- a/src/gromacs/gmxana/gmx_spol.c
+++ b/src/gromacs/gmxana/gmx_spol.c
@@ -36,20 +36,19 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gstat.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxana/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.c
index cf72122974..b676ffc6a2 100644
--- a/src/gromacs/gmxana/gmx_tcaf.c
+++ b/src/gromacs/gmxana/gmx_tcaf.c
@@ -40,24 +40,24 @@
 #include <stdio.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 #define NK  24
diff --git a/src/gromacs/gmxana/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.c
index 86e9a006f9..cd3d0b5ccf 100644
--- a/src/gromacs/gmxana/gmx_traj.c
+++ b/src/gromacs/gmxana/gmx_traj.c
@@ -41,23 +41,22 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void low_print_data(FILE *fp, real time, rvec x[], int n, atom_id *index,
                            gmx_bool bDim[], const char *sffmt)
diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
index 5a011c992c..e13434df55 100644
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.c
@@ -40,27 +40,26 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define TIME_EXPLICIT 0
 #define TIME_CONTINUE 1
diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
index f0aa6b5d80..4a0be11681 100644
--- a/src/gromacs/gmxana/gmx_trjconv.c
+++ b/src/gromacs/gmxana/gmx_trjconv.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
diff --git a/src/gromacs/gmxana/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.c
index bdf5cb3569..ed383bf2f4 100644
--- a/src/gromacs/gmxana/gmx_trjorder.c
+++ b/src/gromacs/gmxana/gmx_trjorder.c
@@ -41,22 +41,20 @@
 #include <string.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/xvgr.h"
-
 #include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     atom_id i;
diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index 990ec4738d..b9c2af3e71 100644
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -34,11 +34,11 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <stdlib.h>
 #include <time.h>
 
-#include "config.h"
-
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
diff --git a/src/gromacs/gmxana/gmx_vanhove.c b/src/gromacs/gmxana/gmx_vanhove.c
index 781fc5cf1f..fb372b77e1 100644
--- a/src/gromacs/gmxana/gmx_vanhove.c
+++ b/src/gromacs/gmxana/gmx_vanhove.c
@@ -41,21 +41,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 int gmx_vanhove(int argc, char *argv[])
diff --git a/src/gromacs/gmxana/gmx_velacc.c b/src/gromacs/gmxana/gmx_velacc.c
index b6567a4813..34c378d3a4 100644
--- a/src/gromacs/gmxana/gmx_velacc.c
+++ b/src/gromacs/gmxana/gmx_velacc.c
@@ -40,24 +40,24 @@
 #include <stdio.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fft/fft.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gstat.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void index_atom2mol(int *n, atom_id *index, t_block *mols)
 {
diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
index eea3606495..7a5b0a4333 100644
--- a/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@ -53,19 +53,18 @@
 #include <sstream>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
-#include "gmx_ana.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/xvgr.h"
-
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 //! longest file names allowed in input files
 #define WHAM_MAXFILELEN 2048
diff --git a/src/gromacs/gmxana/gmx_wheel.c b/src/gromacs/gmxana/gmx_wheel.c
index d990df1180..457b1a17a0 100644
--- a/src/gromacs/gmxana/gmx_wheel.c
+++ b/src/gromacs/gmxana/gmx_wheel.c
@@ -41,19 +41,18 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/fileio/writeps.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "gstat.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/strdb.h"
-#include "gromacs/fileio/writeps.h"
+#include "gromacs/utility/smalloc.h"
 
 static gmx_bool *bPhobics(int nres, char *resnm[])
 {
diff --git a/src/gromacs/gmxana/gmx_xpm2ps.c b/src/gromacs/gmxana/gmx_xpm2ps.c
index 0e2bd1f676..53c67ac016 100644
--- a/src/gromacs/gmxana/gmx_xpm2ps.c
+++ b/src/gromacs/gmxana/gmx_xpm2ps.c
@@ -36,21 +36,21 @@
  */
 #include "gmxpre.h"
 
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <math.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/writeps.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define FUDGE 1.2
 #define DDD   2
diff --git a/src/gromacs/gmxana/gstat.h b/src/gromacs/gmxana/gstat.h
index 0d490d9ab1..a07b3ed513 100644
--- a/src/gromacs/gmxana/gstat.h
+++ b/src/gromacs/gmxana/gstat.h
@@ -37,10 +37,10 @@
 #ifndef GMX_GMXANA_GSTAT_H
 #define GMX_GMXANA_GSTAT_H
 
-#include "../legacyheaders/typedefs.h"
-#include "../legacyheaders/oenv.h"
-#include "../commandline/pargs.h"
-#include "../topology/index.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/topology/index.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxana/hxprops.c b/src/gromacs/gmxana/hxprops.c
index bad612044a..57acd55c76 100644
--- a/src/gromacs/gmxana/hxprops.c
+++ b/src/gromacs/gmxana/hxprops.c
@@ -36,19 +36,19 @@
  */
 #include "gmxpre.h"
 
+#include "hxprops.h"
+
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/bonded/bonded.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
-#include "hxprops.h"
-#include "gromacs/utility/smalloc.h"
-
-#include "gromacs/bonded/bonded.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 real ellipticity(int nres, t_bb bb[])
 {
diff --git a/src/gromacs/gmxana/hxprops.h b/src/gromacs/gmxana/hxprops.h
index 1229b5e580..c6242d76b7 100644
--- a/src/gromacs/gmxana/hxprops.h
+++ b/src/gromacs/gmxana/hxprops.h
@@ -39,6 +39,7 @@
 #define _hxprops_h
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 #define PHI_AHX (-55.0)
diff --git a/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp b/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp
index 7c96a96f3c..4af681f2f6 100644
--- a/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp
+++ b/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp
@@ -41,12 +41,13 @@
 
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include "gromacs/gmxana/gmx_ana.h"
-#include "testutils/integrationtests.h"
-#include "testutils/cmdlinetest.h"
 #include "gromacs/utility/arrayref.h"
 
-#include "config.h"
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
 
 namespace
 {
diff --git a/src/gromacs/gmxana/nrama.c b/src/gromacs/gmxana/nrama.c
index a69fc8a3bd..0c34aeeca7 100644
--- a/src/gromacs/gmxana/nrama.c
+++ b/src/gromacs/gmxana/nrama.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "nrama.h"
+
 #include <math.h>
 #include <stdlib.h>
 
-#include "nrama.h"
-
 #include "gromacs/bonded/bonded.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/pbcutil/rmpbc.h"
 
 static const char *pp_pat[] = { "C", "N", "CA", "C", "N" };
 #define NPP (sizeof(pp_pat)/sizeof(pp_pat[0]))
diff --git a/src/gromacs/gmxana/nrama.h b/src/gromacs/gmxana/nrama.h
index 901c0847c6..03ee814181 100644
--- a/src/gromacs/gmxana/nrama.h
+++ b/src/gromacs/gmxana/nrama.h
@@ -38,9 +38,9 @@
 #ifndef GMX_GMXANA_NRAMA_H
 #define GMX_GMXANA_NRAMA_H
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/legacyheaders/oenv.h"
-#include "../fileio/trxio.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxana/polynomials.c b/src/gromacs/gmxana/polynomials.c
index 91cd15ff89..9f6257bfbe 100644
--- a/src/gromacs/gmxana/polynomials.c
+++ b/src/gromacs/gmxana/polynomials.c
@@ -36,11 +36,12 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
 #include <math.h>
+#include <stdio.h>
+
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gstat.h"
 
 real LegendreP(real x, unsigned long m)
 
diff --git a/src/gromacs/gmxana/powerspect.c b/src/gromacs/gmxana/powerspect.c
index 071e50afad..67674959c7 100644
--- a/src/gromacs/gmxana/powerspect.c
+++ b/src/gromacs/gmxana/powerspect.c
@@ -35,12 +35,13 @@
 
 #include "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
+#include "powerspect.h"
+
 #include "gromacs/fft/fft.h"
+#include "gromacs/gmxana/interf.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "interf.h"
-#include "powerspect.h"
+#include "gromacs/utility/smalloc.h"
 
 void addtoavgenergy(t_complex *list, real *result, int size, int tsteps)
 {
diff --git a/src/gromacs/gmxana/powerspect.h b/src/gromacs/gmxana/powerspect.h
index 9f64cc5cfe..5f9bbc3241 100644
--- a/src/gromacs/gmxana/powerspect.h
+++ b/src/gromacs/gmxana/powerspect.h
@@ -36,8 +36,8 @@
 #ifndef _powerspect_h
 #define _powerspect_h
 
+#include "gromacs/gmxana/interf.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "interf.h"
 
 #ifdef __cplusplus
 extern "C"
diff --git a/src/gromacs/gmxana/pp2shift.c b/src/gromacs/gmxana/pp2shift.c
index 4c7fdb951d..fa12f6d0b6 100644
--- a/src/gromacs/gmxana/pp2shift.c
+++ b/src/gromacs/gmxana/pp2shift.c
@@ -36,17 +36,18 @@
  */
 #include "gmxpre.h"
 
-#include <stdlib.h>
 #include <math.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/units.h"
-#include "gromacs/utility/smalloc.h"
-#include "gstat.h"
+#include <stdlib.h>
+
 #include "gromacs/fileio/matio.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     int    nx, ny;
diff --git a/src/gromacs/gmxana/princ.c b/src/gromacs/gmxana/princ.c
index e3906590a4..fb7dcad1d7 100644
--- a/src/gromacs/gmxana/princ.c
+++ b/src/gromacs/gmxana/princ.c
@@ -37,13 +37,13 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "princ.h"
 
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
 
 static void m_op(matrix mat, rvec x)
 {
diff --git a/src/gromacs/gmxana/sfactor.c b/src/gromacs/gmxana/sfactor.c
index 8d027fe4a5..8cc7492d77 100644
--- a/src/gromacs/gmxana/sfactor.c
+++ b/src/gromacs/gmxana/sfactor.c
@@ -36,22 +36,23 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/topology/index.h"
+#include "sfactor.h"
+
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "sfactor.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 typedef struct gmx_structurefactors {
diff --git a/src/gromacs/gmxana/sfactor.h b/src/gromacs/gmxana/sfactor.h
index 9df62afd88..0550909596 100644
--- a/src/gromacs/gmxana/sfactor.h
+++ b/src/gromacs/gmxana/sfactor.h
@@ -37,9 +37,9 @@
 #ifndef _sfactor_h
 #define _sfactor_h
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "../math/gmxcomplex.h"
 #include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/gmxcomplex.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxlib/calcgrid.c b/src/gromacs/gmxlib/calcgrid.c
index 62d25e1ce8..1de1f57efe 100644
--- a/src/gromacs/gmxlib/calcgrid.c
+++ b/src/gromacs/gmxlib/calcgrid.c
@@ -36,12 +36,13 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/calcgrid.h"
+
 #include <math.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/utility/smalloc.h"
 
 /* The grid sizes below are based on timing of a 3D cubic grid in fftw
  * compiled with SSE using 4 threads in fft5d.c.
diff --git a/src/gromacs/gmxlib/chargegroup.c b/src/gromacs/gmxlib/chargegroup.c
index 00dbf09dcf..41e152518d 100644
--- a/src/gromacs/gmxlib/chargegroup.c
+++ b/src/gromacs/gmxlib/chargegroup.c
@@ -36,13 +36,15 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/chargegroup.h"
+
 #include <math.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/utility/smalloc.h"
 
 
 void calc_chargegroup_radii(const gmx_mtop_t *mtop, rvec *x,
diff --git a/src/gromacs/gmxlib/checkpoint.cpp b/src/gromacs/gmxlib/checkpoint.cpp
index bec5b71652..c1a806c42d 100644
--- a/src/gromacs/gmxlib/checkpoint.cpp
+++ b/src/gromacs/gmxlib/checkpoint.cpp
@@ -39,6 +39,8 @@
 
 #include "gromacs/legacyheaders/checkpoint.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <stdlib.h>
 #include <string.h>
@@ -46,8 +48,6 @@
 
 #include <fcntl.h>
 
-#include "config.h"
-
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
diff --git a/src/gromacs/gmxlib/conformation-utilities.c b/src/gromacs/gmxlib/conformation-utilities.c
index 59f433fa5d..d21efa4cde 100644
--- a/src/gromacs/gmxlib/conformation-utilities.c
+++ b/src/gromacs/gmxlib/conformation-utilities.c
@@ -40,6 +40,7 @@
 #include "conformation-utilities.h"
 
 #include <math.h>
+
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
diff --git a/src/gromacs/gmxlib/conformation-utilities.h b/src/gromacs/gmxlib/conformation-utilities.h
index 8aa337b69c..0fbe271f04 100644
--- a/src/gromacs/gmxlib/conformation-utilities.h
+++ b/src/gromacs/gmxlib/conformation-utilities.h
@@ -37,9 +37,9 @@
 #ifndef GMX_CONFORMATION_UTILITIES_H
 #define GMX_CONFORMATION_UTILITIES_H
 
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxlib/copyrite.cpp b/src/gromacs/gmxlib/copyrite.cpp
index c1b94f0ebe..fe7045a22e 100644
--- a/src/gromacs/gmxlib/copyrite.cpp
+++ b/src/gromacs/gmxlib/copyrite.cpp
@@ -38,13 +38,13 @@
 
 #include "gromacs/legacyheaders/copyrite.h"
 
+#include "config.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
 
-#include "config.h"
-
 #ifdef HAVE_LIBMKL
 #include <mkl.h>
 #endif
diff --git a/src/gromacs/gmxlib/cuda_tools/copyrite_gpu.cu b/src/gromacs/gmxlib/cuda_tools/copyrite_gpu.cu
index 76f9222412..4b5bca9d6f 100644
--- a/src/gromacs/gmxlib/cuda_tools/copyrite_gpu.cu
+++ b/src/gromacs/gmxlib/cuda_tools/copyrite_gpu.cu
@@ -36,6 +36,7 @@
 #include "gmxpre.h"
 
 #include <stdio.h>
+
 #include <cuda.h>
 #include <cuda_runtime_api.h>
 
diff --git a/src/gromacs/gmxlib/cuda_tools/cudautils.cu b/src/gromacs/gmxlib/cuda_tools/cudautils.cu
index f92a53f07d..44a18eaec4 100644
--- a/src/gromacs/gmxlib/cuda_tools/cudautils.cu
+++ b/src/gromacs/gmxlib/cuda_tools/cudautils.cu
@@ -35,11 +35,12 @@
 
 #include "gmxpre.h"
 
+#include "cudautils.cuh"
+
 #include <stdlib.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "cudautils.cuh"
+#include "gromacs/utility/smalloc.h"
 
 /*** Generic CUDA data operation wrappers ***/
 
diff --git a/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu b/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu
index cc221cfe24..d0c684d4ae 100644
--- a/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu
+++ b/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu
@@ -35,11 +35,11 @@
 
 #include "gmxpre.h"
 
-#include <stdlib.h>
-
-#include "cudautils.cuh"
 #include "gromacs/legacyheaders/pmalloc_cuda.h"
 
+#include <stdlib.h>
+
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
 #include "gromacs/utility/cstringutil.h"
 
 /*! Allocates nbytes of page-locked memory.
diff --git a/src/gromacs/gmxlib/disre.c b/src/gromacs/gmxlib/disre.c
index 764e8e1396..8e2fefd24f 100644
--- a/src/gromacs/gmxlib/disre.c
+++ b/src/gromacs/gmxlib/disre.c
@@ -37,25 +37,25 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/disre.h"
+
 #include "config.h"
 
 #include <math.h>
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/topology/mtop_util.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 void init_disres(FILE *fplog, const gmx_mtop_t *mtop,
diff --git a/src/gromacs/gmxlib/ewald_util.c b/src/gromacs/gmxlib/ewald_util.c
index 44dc2271f3..d3bb07b6e3 100644
--- a/src/gromacs/gmxlib/ewald_util.c
+++ b/src/gromacs/gmxlib/ewald_util.c
@@ -36,19 +36,20 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
 #include <math.h>
-#include "gromacs/math/utilities.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/smalloc.h"
 
 real calc_ewaldcoeff_q(real rc, real dtol)
 {
diff --git a/src/gromacs/gmxlib/gmx_cpuid.c b/src/gromacs/gmxlib/gmx_cpuid.c
index 0e69251321..18109192d9 100644
--- a/src/gromacs/gmxlib/gmx_cpuid.c
+++ b/src/gromacs/gmxlib/gmx_cpuid.c
@@ -45,10 +45,10 @@
 #  include <sched.h>
 #endif
 
+#include <ctype.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <ctype.h>
 #ifdef GMX_NATIVE_WINDOWS
 /* MSVC definition for __cpuid() */
     #ifdef _MSC_VER
diff --git a/src/gromacs/gmxlib/gmx_detect_hardware.cpp b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
index e05629a512..bc7817d5f6 100644
--- a/src/gromacs/gmxlib/gmx_detect_hardware.cpp
+++ b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
@@ -36,6 +36,8 @@
 
 #include "gromacs/legacyheaders/gmx_detect_hardware.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <errno.h>
 #include <stdlib.h>
@@ -44,8 +46,6 @@
 #include <string>
 #include <vector>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 /* For sysconf */
 #include <unistd.h>
diff --git a/src/gromacs/gmxlib/gmx_omp_nthreads.c b/src/gromacs/gmxlib/gmx_omp_nthreads.c
index 76824dee39..e9a415c403 100644
--- a/src/gromacs/gmxlib/gmx_omp_nthreads.c
+++ b/src/gromacs/gmxlib/gmx_omp_nthreads.c
@@ -35,21 +35,21 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+
+#include "config.h"
+
+#include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <assert.h>
-
-#include "config.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/md_logging.h"
-
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
diff --git a/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu b/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
index 542e3a8fb9..f8b741923e 100644
--- a/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
+++ b/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
@@ -35,15 +35,14 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/gpu_utils.h"
+
+#include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <assert.h>
 
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
 #include "gromacs/legacyheaders/types/hw_info.h"
-
-#include "gromacs/legacyheaders/gpu_utils.h"
-#include "../cuda_tools/cudautils.cuh"
-
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxlib/ifunc.c b/src/gromacs/gmxlib/ifunc.c
index e27b78aa22..5a649c0bb0 100644
--- a/src/gromacs/gmxlib/ifunc.c
+++ b/src/gromacs/gmxlib/ifunc.c
@@ -38,10 +38,10 @@
 #include "gmxpre.h"
 
 #include "gromacs/bonded/bonded.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
 #include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #define  def_bonded(str, lstr, nra, nrpa, nrpb, ind, func) \
     {str, lstr, (nra), (nrpa), (nrpb), IF_BOND,                        (ind), (func)}
diff --git a/src/gromacs/gmxlib/inputrec.c b/src/gromacs/gmxlib/inputrec.c
index d55f8e4ed5..ad48b85814 100644
--- a/src/gromacs/gmxlib/inputrec.c
+++ b/src/gromacs/gmxlib/inputrec.c
@@ -36,9 +36,10 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/inputrec.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
 
 
diff --git a/src/gromacs/gmxlib/main.cpp b/src/gromacs/gmxlib/main.cpp
index a91b41e2e4..9a3078310d 100644
--- a/src/gromacs/gmxlib/main.cpp
+++ b/src/gromacs/gmxlib/main.cpp
@@ -38,14 +38,14 @@
 
 #include "gromacs/legacyheaders/main.h"
 
+#include "config.h"
+
 #include <limits.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
 
-#include "config.h"
-
 #ifdef GMX_NATIVE_WINDOWS
 #include <process.h>
 #endif
diff --git a/src/gromacs/gmxlib/md_logging.c b/src/gromacs/gmxlib/md_logging.c
index 36eb06d964..cee3c06ba6 100644
--- a/src/gromacs/gmxlib/md_logging.c
+++ b/src/gromacs/gmxlib/md_logging.c
@@ -36,10 +36,12 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
+#include "gromacs/legacyheaders/md_logging.h"
+
 #include <stdarg.h>
+#include <stdio.h>
+
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/md_logging.h"
 
 
 void md_print_info(const t_commrec *cr, FILE *fplog,
diff --git a/src/gromacs/gmxlib/mvdata.c b/src/gromacs/gmxlib/mvdata.c
index 8885b13c0e..41aeaeaf15 100644
--- a/src/gromacs/gmxlib/mvdata.c
+++ b/src/gromacs/gmxlib/mvdata.c
@@ -37,16 +37,16 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/mvdata.h"
+
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/tgroup.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/gmxlib/names.c b/src/gromacs/gmxlib/names.c
index 0e048d42db..6e63f2fb62 100644
--- a/src/gromacs/gmxlib/names.c
+++ b/src/gromacs/gmxlib/names.c
@@ -36,9 +36,10 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/names.h"
 
+#include "gromacs/legacyheaders/typedefs.h"
+
 /* note: these arrays should correspond to enums in include/types/enums.h */
 
 const char *epbc_names[epbcNR+1] =
diff --git a/src/gromacs/gmxlib/network.c b/src/gromacs/gmxlib/network.c
index f43d778943..94905661e1 100644
--- a/src/gromacs/gmxlib/network.c
+++ b/src/gromacs/gmxlib/network.c
@@ -45,10 +45,9 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/gmxlib/nonbonded/nb_free_energy.c b/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
index 35175bc217..93f1d1c361 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "nb_free_energy.h"
+
 #include <math.h>
 
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "nb_kernel.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "nb_free_energy.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
 
 void
diff --git a/src/gromacs/gmxlib/nonbonded/nb_free_energy.h b/src/gromacs/gmxlib/nonbonded/nb_free_energy.h
index efc98d173e..8b76221810 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_free_energy.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_free_energy.h
@@ -38,7 +38,7 @@
 #ifndef _nb_free_energy_h_
 #define _nb_free_energy_h_
 
-#include "nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
 
 void
diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic.c b/src/gromacs/gmxlib/nonbonded/nb_generic.c
index dca18ad4fa..55fdb28a01 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_generic.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic.c
@@ -36,19 +36,18 @@
  */
 #include "gmxpre.h"
 
+#include "nb_generic.h"
+
 #include <math.h>
 
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nb_generic.h"
-#include "gromacs/legacyheaders/nrnb.h"
-
 #include "gromacs/utility/fatalerror.h"
 
-#include "gromacs/legacyheaders/nonbonded.h"
-#include "nb_kernel.h"
-
 void
 gmx_nb_generic_kernel(t_nblist *                nlist,
                       rvec *                    xx,
diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic.h b/src/gromacs/gmxlib/nonbonded/nb_generic.h
index d68aebe1b8..65785f2bda 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_generic.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic.h
@@ -38,9 +38,9 @@
 #ifndef _nb_generic_h_
 #define _nb_generic_h_
 
-#include "nb_kernel.h"
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 gmx_nb_generic_kernel(t_nblist *                nlist,
diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
index eedffd8645..4334a04c7a 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
@@ -36,19 +36,18 @@
  */
 #include "gmxpre.h"
 
+#include "nb_generic_adress.h"
+
 #include <math.h>
 
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nb_generic_adress.h"
-#include "gromacs/legacyheaders/nrnb.h"
-
 #include "gromacs/utility/fatalerror.h"
 
-#include "gromacs/legacyheaders/nonbonded.h"
-#include "nb_kernel.h"
-
 #define ALMOST_ZERO 1e-30
 #define ALMOST_ONE 1-(1e-30)
 void
diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.h b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.h
index 17eabeeb29..fd838f2e63 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.h
@@ -38,9 +38,9 @@
 #ifndef _nb_generic_adress_h_
 #define _nb_generic_adress_h_
 
-#include "nb_kernel.h"
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 gmx_nb_generic_adress_kernel(t_nblist *                nlist,
diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
index 97c43c2b0b..fe14f9586a 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "nb_generic_cg.h"
+
 #include <math.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nb_generic_cg.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "nb_kernel.h"
 #include "gromacs/legacyheaders/nrnb.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
 
 void
diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.h b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.h
index fa4e25768d..2ef87893d8 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.h
@@ -38,10 +38,10 @@
 #ifndef _nb_generic_cg_h_
 #define _nb_generic_cg_h_
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 gmx_nb_generic_cg_kernel(t_nblist *                nlist,
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel.c b/src/gromacs/gmxlib/nonbonded/nb_kernel.c
index 60f73652a2..29b01659bc 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel.c
@@ -34,13 +34,14 @@
  */
 #include "gmxpre.h"
 
+#include "nb_kernel.h"
+
 #include <stdio.h>
 #include <string.h>
 
-#include "nb_kernel.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* Static data structures to find kernels */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel.h b/src/gromacs/gmxlib/nonbonded/nb_kernel.h
index c5d489949a..76f884aa86 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel.h
@@ -43,8 +43,8 @@ extern "C" {
 #endif
 
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 /* Structure to collect kernel data not available in forcerec or mdatoms structures.
  * This is only used inside the nonbonded module.
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/kernelutil_x86_avx_128_fma_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/kernelutil_x86_avx_128_fma_double.h
index 5b931327a5..dba59bbf0e 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/kernelutil_x86_avx_128_fma_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/kernelutil_x86_avx_128_fma_double.h
@@ -36,6 +36,7 @@
 #define _kernelutil_x86_avx_128_fma_double_h_
 
 #include <math.h>
+
 #include <immintrin.h>
 #ifdef _MSC_VER
 #    include <intrin.h>
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
index bfadf92430..e12ba84a31 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_128_fma_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_128_fma_double;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h
index 14c3771d7e..e6f9e12486 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_avx_128_fma_double_h
 #define nb_kernel_avx_128_fma_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
index 1715f97cbc..6aadac8d35 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
@@ -38,6 +38,7 @@
 #include "config.h"
 
 #include <math.h>
+
 #include <immintrin.h>
 #ifdef _MSC_VER
 #    include <intrin.h>
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
index 1a7c473b67..9dfb2dcf53 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_128_fma_single;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_128_fma_single;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h
index 8c2387aa36..a96f66b81e 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_avx_128_fma_single_h
 #define nb_kernel_avx_128_fma_single_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
index dfa412bf84..b536da526a 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_256_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_256_double;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h
index 308256944e..97a60c168e 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_avx_256_double_h
 #define nb_kernel_avx_256_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
index 77093dad3f..0215594956 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_256_single;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_256_single;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h
index 35c2c3b514..bcbb42de55 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_avx_256_single_h
 #define nb_kernel_avx_256_single_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
index 0c0dcb7205..92335ff0c0 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
@@ -36,18 +36,17 @@
  */
 #include "gmxpre.h"
 
+#include "nb_kernel_allvsall.h"
+
 #include "config.h"
 
 #include <math.h>
 
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/simple.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nb_kernel_allvsall.h"
-#include "gromacs/legacyheaders/nrnb.h"
-
 typedef struct
 {
     real **    pvdwparam;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.h
index bf5e34b4bb..62b60ca939 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.h
@@ -37,9 +37,9 @@
 
 #include "config.h"
 
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../nb_kernel.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 nb_kernel_allvsall(t_nblist *                nlist,
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
index 3557e825e6..be401ee7bc 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
@@ -36,18 +36,17 @@
  */
 #include "gmxpre.h"
 
+#include "nb_kernel_allvsallgb.h"
+
 #include "config.h"
 
 #include <math.h>
 
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/simple.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nb_kernel_allvsallgb.h"
-#include "gromacs/legacyheaders/nrnb.h"
-
 typedef struct
 {
     real **    pvdwparam;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h
index 6083fb2295..318b103008 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h
@@ -37,9 +37,9 @@
 
 #include "config.h"
 
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../nb_kernel.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 void
 nb_kernel_allvsallgb(t_nblist *                nlist,
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
index 361dd233a0..ca9b753a79 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_c;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_c;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h
index 32640c7d44..e524079cd6 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_c_h
 #define nb_kernel_c_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c
index c63a233ef7..bd2e022fe8 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sparc64_hpc_ace_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sparc64_hpc_ace_double;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h
index 67ace2f0e7..a18c885757 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sparc64_hpc_ace_double_h
 #define nb_kernel_sparc64_hpc_ace_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/kernelutil_x86_sse2_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/kernelutil_x86_sse2_double.h
index 415fee6de3..4885d6df1a 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/kernelutil_x86_sse2_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/kernelutil_x86_sse2_double.h
@@ -35,11 +35,11 @@
 #ifndef _kernelutil_x86_sse2_double_h_
 #define _kernelutil_x86_sse2_double_h_
 
+#include "config.h"
+
 #include <math.h>
 #include <stdio.h>
 
-#include "config.h"
-
 
 /* Normal sum of four ymm registers */
 #define gmx_mm_sum4_pd(t0, t1, t2, t3)  _mm_add_pd(_mm_add_pd(t0, t1), _mm_add_pd(t2, t3))
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
index 02ce4ef417..ce36e1c56d 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse2_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse2_double;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h
index 1720d436fc..3d45667bd2 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sse2_double_h
 #define nb_kernel_sse2_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h
index 31f1230c80..3356a780c1 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/kernelutil_x86_sse2_single.h
@@ -37,10 +37,10 @@
 
 /* We require SSE2 now! */
 
-#include <math.h>
-
 #include "config.h"
 
+#include <math.h>
+
 #define gmx_mm_castsi128_ps   _mm_castsi128_ps
 
 #define gmx_mm_extract_epi32(x, imm) _mm_cvtsi128_si32(_mm_srli_si128((x), 4 * (imm)))
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
index a66eb382cd..3bff2be8b3 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse2_single;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse2_single;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h
index 331870820c..82b0ca887b 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sse2_single_h
 #define nb_kernel_sse2_single_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/kernelutil_x86_sse4_1_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/kernelutil_x86_sse4_1_double.h
index a235cd48bc..449fe3666e 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/kernelutil_x86_sse4_1_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/kernelutil_x86_sse4_1_double.h
@@ -35,11 +35,11 @@
 #ifndef _kernelutil_x86_sse4_1_double_h_
 #define _kernelutil_x86_sse4_1_double_h_
 
+#include "config.h"
+
 #include <math.h>
 #include <stdio.h>
 
-#include "config.h"
-
 #define gmx_mm_extract_epi32(x, imm) _mm_extract_epi32((x), (imm))
 #define gmx_mm_castsi128_pd(a) _mm_castsi128_pd(a)
 
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
index c30d800547..2a7f2fc9f7 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse4_1_double;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse4_1_double;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h
index 49113b2ab6..4137318841 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sse4_1_double_h
 #define nb_kernel_sse4_1_double_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/kernelutil_x86_sse4_1_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/kernelutil_x86_sse4_1_single.h
index 2d83de317a..7028cef224 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/kernelutil_x86_sse4_1_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/kernelutil_x86_sse4_1_single.h
@@ -35,10 +35,10 @@
 #ifndef _kernelutil_x86_sse4_1_single_h_
 #define _kernelutil_x86_sse4_1_single_h_
 
-#include <math.h>
-
 #include "config.h"
 
+#include <math.h>
+
 #undef gmx_restrict
 #define gmx_restrict
 
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
index 95b0055d6b..79546e1b1b 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
@@ -37,7 +37,7 @@
  */
 #include "gmxpre.h"
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse4_1_single;
 nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse4_1_single;
diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h
index c70ec17440..22160f86a2 100644
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef nb_kernel_sse4_1_single_h
 #define nb_kernel_sse4_1_single_h
 
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 
 
 /* List of kernels for this architecture with metadata about them */
diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.c b/src/gromacs/gmxlib/nonbonded/nonbonded.c
index baaf1184f2..7bcf2a66b1 100644
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.c
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.c
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/nonbonded.h"
+
 #include "config.h"
 
 #include <stdio.h>
@@ -44,61 +46,57 @@
 #include "thread_mpi/threads.h"
 
 #include "gromacs/bonded/bonded.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_adress.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_cg.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/nonbonded.h"
-#include "gromacs/simd/simd.h"
-
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/simd/simd.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nb_kernel.h"
-#include "nb_free_energy.h"
-#include "nb_generic.h"
-#include "nb_generic_cg.h"
-#include "nb_generic_adress.h"
-
 /* Different default (c) and SIMD instructions interaction-specific kernels */
-#include "nb_kernel_c/nb_kernel_c.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h"
 
 #if (defined GMX_SIMD_X86_SSE2) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_sse2_single/nb_kernel_sse2_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE4_1) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER) && !(defined GMX_DOUBLE)
-#    include "nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE2 && defined GMX_DOUBLE)
-#    include "nb_kernel_sse2_double/nb_kernel_sse2_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h"
 #endif
 #if (defined GMX_SIMD_X86_SSE4_1 && defined GMX_DOUBLE)
-#    include "nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_128_FMA && defined GMX_DOUBLE)
-#    include "nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
 #endif
 #if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER && defined GMX_DOUBLE)
-#    include "nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
 #endif
 #if (defined GMX_SIMD_SPARC64_HPC_ACE && defined GMX_DOUBLE)
-#    include "nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
+#    include "gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
 #endif
 
 
diff --git a/src/gromacs/gmxlib/nrnb.c b/src/gromacs/gmxlib/nrnb.c
index 54925d85ed..f77bd43a80 100644
--- a/src/gromacs/gmxlib/nrnb.c
+++ b/src/gromacs/gmxlib/nrnb.c
@@ -36,13 +36,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/nrnb.h"
+
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/smalloc.h"
 
 typedef struct {
diff --git a/src/gromacs/gmxlib/oenv.cpp b/src/gromacs/gmxlib/oenv.cpp
index d7fcc05037..89201b8064 100644
--- a/src/gromacs/gmxlib/oenv.cpp
+++ b/src/gromacs/gmxlib/oenv.cpp
@@ -38,10 +38,9 @@
 
 #include "gromacs/legacyheaders/oenv.h"
 
-#include "gromacs/utility/smalloc.h"
-
-#include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 
 struct output_env
 {
diff --git a/src/gromacs/gmxlib/orires.c b/src/gromacs/gmxlib/orires.c
index 3c4f3e5db5..1d15a6a4cc 100644
--- a/src/gromacs/gmxlib/orires.c
+++ b/src/gromacs/gmxlib/orires.c
@@ -36,20 +36,20 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
 
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxlib/rbin.c b/src/gromacs/gmxlib/rbin.c
index 5ef4d5d229..754c648cb2 100644
--- a/src/gromacs/gmxlib/rbin.c
+++ b/src/gromacs/gmxlib/rbin.c
@@ -37,9 +37,10 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/rbin.h"
+
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/smalloc.h"
 
 t_bin *mk_bin(void)
diff --git a/src/gromacs/gmxlib/readinp.c b/src/gromacs/gmxlib/readinp.c
index 0f2e4196d7..10a2c7cc36 100644
--- a/src/gromacs/gmxlib/readinp.c
+++ b/src/gromacs/gmxlib/readinp.c
@@ -36,18 +36,20 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/readinp.h"
+
 #include <stdio.h>
 #include <stdlib.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/legacyheaders/macros.h"
+
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 t_inpfile *read_inpfile(const char *fn, int *ninp,
                         warninp_t wi)
diff --git a/src/gromacs/gmxlib/sighandler.c b/src/gromacs/gmxlib/sighandler.c
index 2149787465..75ff86caba 100644
--- a/src/gromacs/gmxlib/sighandler.c
+++ b/src/gromacs/gmxlib/sighandler.c
@@ -36,13 +36,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/sighandler.h"
+
 #include "config.h"
 
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/sighandler.h"
 
 const char *gmx_stop_cond_name[] =
 {
diff --git a/src/gromacs/gmxlib/splitter.c b/src/gromacs/gmxlib/splitter.c
index b9557b54a7..cb2eb90f6b 100644
--- a/src/gromacs/gmxlib/splitter.c
+++ b/src/gromacs/gmxlib/splitter.c
@@ -43,7 +43,6 @@
 #include <string.h>
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/idef.h"
diff --git a/src/gromacs/gmxlib/txtdump.c b/src/gromacs/gmxlib/txtdump.c
index b8d3088c73..9b3eec687e 100644
--- a/src/gromacs/gmxlib/txtdump.c
+++ b/src/gromacs/gmxlib/txtdump.c
@@ -38,16 +38,16 @@
 
 /* This file is completely threadsafe - please keep it that way! */
 
+#include "gromacs/legacyheaders/txtdump.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxlib/viewit.c b/src/gromacs/gmxlib/viewit.c
index c728453439..c6a3a690bb 100644
--- a/src/gromacs/gmxlib/viewit.c
+++ b/src/gromacs/gmxlib/viewit.c
@@ -44,9 +44,9 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 
diff --git a/src/gromacs/gmxlib/warninp.c b/src/gromacs/gmxlib/warninp.c
index 9d9b5b79b6..1721a47012 100644
--- a/src/gromacs/gmxlib/warninp.c
+++ b/src/gromacs/gmxlib/warninp.c
@@ -36,13 +36,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/warninp.h"
+
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct warninp {
     gmx_bool bAllowWarnings;
diff --git a/src/gromacs/gmxpreprocess/add_par.c b/src/gromacs/gmxpreprocess/add_par.c
index 26926a91d4..cf471c4641 100644
--- a/src/gromacs/gmxpreprocess/add_par.c
+++ b/src/gromacs/gmxpreprocess/add_par.c
@@ -38,14 +38,15 @@
 #include "gmxpre.h"
 
 #include <string.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "grompp-impl.h"
+
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "toputil.h"
-#include "hackblock.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void clear_atom_list(int i0, atom_id a[])
 {
diff --git a/src/gromacs/gmxpreprocess/add_par.h b/src/gromacs/gmxpreprocess/add_par.h
index ae2b2eca0d..92a0d8be4d 100644
--- a/src/gromacs/gmxpreprocess/add_par.h
+++ b/src/gromacs/gmxpreprocess/add_par.h
@@ -38,8 +38,8 @@
 #ifndef GMX_GMXPREPROCESS_ADD_PAR_H
 #define GMX_GMXPREPROCESS_ADD_PAR_H
 
+#include "gromacs/gmxpreprocess/pdb2top.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "pdb2top.h"
 
 #ifdef __cplusplus
 extern "C"
diff --git a/src/gromacs/gmxpreprocess/addconf.c b/src/gromacs/gmxpreprocess/addconf.c
index b2d1f3a751..7a6e0b0b7f 100644
--- a/src/gromacs/gmxpreprocess/addconf.c
+++ b/src/gromacs/gmxpreprocess/addconf.c
@@ -41,20 +41,19 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxpreprocess/calc_verletbuf.c b/src/gromacs/gmxpreprocess/calc_verletbuf.c
index 8d1313a408..dbdcab9074 100644
--- a/src/gromacs/gmxpreprocess/calc_verletbuf.c
+++ b/src/gromacs/gmxpreprocess/calc_verletbuf.c
@@ -34,20 +34,20 @@
  */
 #include "gmxpre.h"
 
+#include "calc_verletbuf.h"
+
 #include <assert.h>
 #include <math.h>
 #include <stdlib.h>
 
 #include <sys/types.h>
 
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "calc_verletbuf.h"
-#include "../mdlib/nbnxn_consts.h"
-
+#include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxpreprocess/calch.c b/src/gromacs/gmxpreprocess/calch.c
index dfab85b064..d171bbd34b 100644
--- a/src/gromacs/gmxpreprocess/calch.c
+++ b/src/gromacs/gmxpreprocess/calch.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
 #include "calch.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
-
 #include "gromacs/utility/fatalerror.h"
 
 #define xAI xa[0]
diff --git a/src/gromacs/gmxpreprocess/compute_io.c b/src/gromacs/gmxpreprocess/compute_io.c
index 8de74782b7..51a73d1a84 100644
--- a/src/gromacs/gmxpreprocess/compute_io.c
+++ b/src/gromacs/gmxpreprocess/compute_io.c
@@ -38,6 +38,7 @@
 
 #include <signal.h>
 #include <stdlib.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 static int div_nsteps(int nsteps, int nst)
diff --git a/src/gromacs/gmxpreprocess/convparm.c b/src/gromacs/gmxpreprocess/convparm.c
index 3ae40c2a84..e3bac95963 100644
--- a/src/gromacs/gmxpreprocess/convparm.c
+++ b/src/gromacs/gmxpreprocess/convparm.c
@@ -37,20 +37,21 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "convparm.h"
+
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "topio.h"
-#include "toputil.h"
-#include "convparm.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gpp_atomtype.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/utility/smalloc.h"
 
 static int round_check(real r, int limit, int ftype, const char *name)
 {
diff --git a/src/gromacs/gmxpreprocess/fflibutil.cpp b/src/gromacs/gmxpreprocess/fflibutil.cpp
index b47aa18b7c..e87fb8f659 100644
--- a/src/gromacs/gmxpreprocess/fflibutil.cpp
+++ b/src/gromacs/gmxpreprocess/fflibutil.cpp
@@ -36,6 +36,8 @@
 
 #include "fflibutil.h"
 
+#include "config.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -44,8 +46,6 @@
 #include <sys/stat.h>
 #include <sys/types.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
diff --git a/src/gromacs/gmxpreprocess/fflibutil.h b/src/gromacs/gmxpreprocess/fflibutil.h
index f49d96327b..6703c2b7b0 100644
--- a/src/gromacs/gmxpreprocess/fflibutil.h
+++ b/src/gromacs/gmxpreprocess/fflibutil.h
@@ -37,6 +37,7 @@
 #define GMX_GMXPREPROCESS_FFLIBUTIL_H
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
diff --git a/src/gromacs/gmxpreprocess/gen_ad.c b/src/gromacs/gmxpreprocess/gen_ad.c
index c110bc7a3e..61dc0f9cd7 100644
--- a/src/gromacs/gmxpreprocess/gen_ad.c
+++ b/src/gromacs/gmxpreprocess/gen_ad.c
@@ -37,24 +37,24 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gen_ad.h"
+
 #include <ctype.h>
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/cstringutil.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/vec.h"
-#include "toputil.h"
-#include "topio.h"
-#include "gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "pgutil.h"
-#include "resall.h"
-#include "gen_ad.h"
+#include "gromacs/utility/smalloc.h"
 
 #define DIHEDRAL_WAS_SET_IN_RTP 0
 static gmx_bool was_dihedral_set_in_rtp(t_param *dih)
diff --git a/src/gromacs/gmxpreprocess/gen_ad.h b/src/gromacs/gmxpreprocess/gen_ad.h
index a2829d7ad3..e8814a5cab 100644
--- a/src/gromacs/gmxpreprocess/gen_ad.h
+++ b/src/gromacs/gmxpreprocess/gen_ad.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_GEN_AD_H
 #define GMX_GMXPREPROCESS_GEN_AD_H
 
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "toputil.h"
-#include "gpp_nextnb.h"
-#include "resall.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
index 609650f4a1..02522be85f 100644
--- a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
+++ b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
@@ -36,14 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "gen_maxwell_velocities.h"
+
 #include <math.h>
-#include "gromacs/random/random.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
+
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gen_maxwell_velocities.h"
+#include "gromacs/random/random.h"
 #include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/smalloc.h"
 
 static void low_mspeed(real tempi,
                        gmx_mtop_t *mtop, rvec v[], gmx_rng_t rng)
diff --git a/src/gromacs/gmxpreprocess/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
index 9743f690a6..4d0e990044 100644
--- a/src/gromacs/gmxpreprocess/gen_vsite.c
+++ b/src/gromacs/gmxpreprocess/gen_vsite.c
@@ -36,26 +36,26 @@
  */
 #include "gmxpre.h"
 
+#include "gen_vsite.h"
+
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gen_vsite.h"
-#include "resall.h"
-#include "add_par.h"
-#include "gromacs/math/vec.h"
-#include "toputil.h"
-#include "gromacs/math/units.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/futil.h"
-#include "gpp_atomtype.h"
-#include "fflibutil.h"
-
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define MAXNAME 32
diff --git a/src/gromacs/gmxpreprocess/gen_vsite.h b/src/gromacs/gmxpreprocess/gen_vsite.h
index 98d668b175..6a350ef709 100644
--- a/src/gromacs/gmxpreprocess/gen_vsite.h
+++ b/src/gromacs/gmxpreprocess/gen_vsite.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_GEN_VSITE_H
 #define GMX_GMXPREPROCESS_GEN_VSITE_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
-#include "hackblock.h"
 
 #ifdef __cplusplus
 extern "C"
diff --git a/src/gromacs/gmxpreprocess/genconf.c b/src/gromacs/gmxpreprocess/genconf.c
index 13ee605036..9f9a57ce8c 100644
--- a/src/gromacs/gmxpreprocess/genconf.c
+++ b/src/gromacs/gmxpreprocess/genconf.c
@@ -38,17 +38,16 @@
 
 #include "genconf.h"
 
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/legacyheaders/names.h"
-#include "sortwater.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/gmxpreprocess/genhydro.c b/src/gromacs/gmxpreprocess/genhydro.c
index 9ac5b4d444..3a85fa1209 100644
--- a/src/gromacs/gmxpreprocess/genhydro.c
+++ b/src/gromacs/gmxpreprocess/genhydro.c
@@ -36,24 +36,24 @@
  */
 #include "gmxpre.h"
 
+#include "genhydro.h"
+
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "calch.h"
-#include "genhydro.h"
-#include "h_db.h"
-#include "ter_db.h"
-#include "resall.h"
-#include "pgutil.h"
+#include "gromacs/gmxpreprocess/calch.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
 #include "gromacs/legacyheaders/network.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static void copy_atom(t_atoms *atoms1, int a1, t_atoms *atoms2, int a2)
diff --git a/src/gromacs/gmxpreprocess/genhydro.h b/src/gromacs/gmxpreprocess/genhydro.h
index ed5b07f37d..9161a33324 100644
--- a/src/gromacs/gmxpreprocess/genhydro.h
+++ b/src/gromacs/gmxpreprocess/genhydro.h
@@ -39,7 +39,7 @@
 #define GMX_GMXPREPROCESS_GENHYDRO_H
 
 #include "gromacs/fileio/pdbio.h"
-#include "hackblock.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/gmxcpp.c b/src/gromacs/gmxpreprocess/gmxcpp.c
index 81795e9805..42fd453757 100644
--- a/src/gromacs/gmxpreprocess/gmxcpp.c
+++ b/src/gromacs/gmxpreprocess/gmxcpp.c
@@ -36,21 +36,23 @@
  */
 #include "gmxpre.h"
 
-#include <sys/types.h>
+#include "gmxcpp.h"
+
+#include <ctype.h>
+#include <errno.h>
+#include <limits.h>
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <math.h>
 #include <string.h>
-#include <errno.h>
-#include <limits.h>
-#include <ctype.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
+#include <sys/types.h>
+
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gmxcpp.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     char *name;
diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.c b/src/gromacs/gmxpreprocess/gpp_atomtype.c
index 8ef380fd04..4a9c932b0f 100644
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.c
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.c
@@ -36,14 +36,14 @@
  */
 #include "gmxpre.h"
 
+#include "gpp_atomtype.h"
+
 #include <math.h>
 #include <string.h>
 
-#include "topdirs.h"
-#include "toputil.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gpp_atomtype.h"
-
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.h b/src/gromacs/gmxpreprocess/gpp_atomtype.h
index 5a902db7af..9dd46548b3 100644
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.h
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.h
@@ -39,8 +39,9 @@
 #define GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
 
 #include <stdio.h>
+
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
index 905308b3be..6a39e71f88 100644
--- a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
+++ b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
@@ -36,9 +36,9 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
 #include "gpp_bond_atomtype.h"
 
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h
index cd88c07a81..c901d9b1f0 100644
--- a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h
+++ b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.h
@@ -39,6 +39,7 @@
 #define GMX_GMXPREPROCESS_GPP_BONDATOMTYPE_H
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.h b/src/gromacs/gmxpreprocess/gpp_nextnb.h
index e06a382417..c5dde3865e 100644
--- a/src/gromacs/gmxpreprocess/gpp_nextnb.h
+++ b/src/gromacs/gmxpreprocess/gpp_nextnb.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_GPP_NEXTNB_H
 #define GMX_GMXPREPROCESS_GPP_NEXTNB_H
 
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/grompp.c b/src/gromacs/gmxpreprocess/grompp.c
index 7e32feb2f6..8a7c681315 100644
--- a/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@ -38,53 +38,52 @@
 
 #include "grompp.h"
 
-#include <sys/types.h>
-#include <math.h>
-#include <string.h>
+#include <assert.h>
 #include <errno.h>
 #include <limits.h>
-#include <assert.h>
+#include <math.h>
+#include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "readir.h"
-#include "toputil.h"
-#include "topio.h"
+#include <sys/types.h>
+
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "readir.h"
-#include "gromacs/legacyheaders/names.h"
-#include "grompp-impl.h"
-#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/splitter.h"
-#include "gromacs/gmxpreprocess/sortwater.h"
-#include "convparm.h"
-#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
-#include "vsite_parm.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "gromacs/gmxpreprocess/convparm.h"
+#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/gmxpreprocess/tomorse.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
+#include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/calcgrid.h"
-#include "add_par.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/legacyheaders/perf_est.h"
-#include "compute_io.h"
-#include "gpp_atomtype.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/legacyheaders/genborn.h"
-#include "calc_verletbuf.h"
-#include "tomorse.h"
-#include "gromacs/imd/imd.h"
-#include "gromacs/utility/cstringutil.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/splitter.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
diff --git a/src/gromacs/gmxpreprocess/h_db.c b/src/gromacs/gmxpreprocess/h_db.c
index 85bacf8a3f..f630ae7876 100644
--- a/src/gromacs/gmxpreprocess/h_db.c
+++ b/src/gromacs/gmxpreprocess/h_db.c
@@ -37,17 +37,18 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "h_db.h"
+
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "h_db.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "fflibutil.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Number of control atoms for each 'add' type.
  *
diff --git a/src/gromacs/gmxpreprocess/h_db.h b/src/gromacs/gmxpreprocess/h_db.h
index f297506765..24f873b6c2 100644
--- a/src/gromacs/gmxpreprocess/h_db.h
+++ b/src/gromacs/gmxpreprocess/h_db.h
@@ -40,7 +40,7 @@
 
 #include <stdio.h>
 
-#include "hackblock.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/hackblock.c b/src/gromacs/gmxpreprocess/hackblock.c
index ff7f0fdf2e..c30a69851b 100644
--- a/src/gromacs/gmxpreprocess/hackblock.c
+++ b/src/gromacs/gmxpreprocess/hackblock.c
@@ -37,12 +37,14 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include <string.h>
 #include "hackblock.h"
+
+#include <string.h>
+
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/names.h"
 
 /* these MUST correspond to the enum in hackblock.h */
 const char *btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };
diff --git a/src/gromacs/gmxpreprocess/hackblock.h b/src/gromacs/gmxpreprocess/hackblock.h
index 52c138ced6..294dcec86c 100644
--- a/src/gromacs/gmxpreprocess/hackblock.h
+++ b/src/gromacs/gmxpreprocess/hackblock.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
 #define GMX_GMXPREPROCESS_HACKBLOCK_H
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/pdbio.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/symtab.h"
 
 #ifdef __cplusplus
diff --git a/src/gromacs/gmxpreprocess/hizzie.c b/src/gromacs/gmxpreprocess/hizzie.c
index e7b637a21b..0aff84f7a4 100644
--- a/src/gromacs/gmxpreprocess/hizzie.c
+++ b/src/gromacs/gmxpreprocess/hizzie.c
@@ -39,16 +39,16 @@
 
 #include <stdio.h>
 #include <string.h>
-#include "gromacs/legacyheaders/typedefs.h"
+
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
-#include "toputil.h"
-#include "pdb2top.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxpreprocess/insert-molecules.cpp b/src/gromacs/gmxpreprocess/insert-molecules.cpp
index 32d5908987..5818fbbbea 100644
--- a/src/gromacs/gmxpreprocess/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/insert-molecules.cpp
@@ -38,18 +38,17 @@
 
 #include "insert-molecules.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/addconf.h"
+#include "gromacs/gmxpreprocess/read-conformation.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "addconf.h"
-#include "read-conformation.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
diff --git a/src/gromacs/gmxpreprocess/nm2type.c b/src/gromacs/gmxpreprocess/nm2type.c
index d4b01a884d..41882302ac 100644
--- a/src/gromacs/gmxpreprocess/nm2type.c
+++ b/src/gromacs/gmxpreprocess/nm2type.c
@@ -37,26 +37,25 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "nm2type.h"
+
 #include <string.h>
 
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "toppush.h"
-#include "pdb2top.h"
-#include "gpp_nextnb.h"
-#include "gpp_atomtype.h"
-#include "fflibutil.h"
-
-#include "nm2type.h"
-
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
 {
diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.c b/src/gromacs/gmxpreprocess/pdb2gmx.c
index 0a1aeb20d4..ac9f6ec083 100644
--- a/src/gromacs/gmxpreprocess/pdb2gmx.c
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.c
@@ -43,40 +43,37 @@
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "toputil.h"
-#include "h_db.h"
-#include "pgutil.h"
-#include "resall.h"
-#include "pdb2top.h"
-#include "ter_db.h"
+#include "gromacs/fileio/strdb.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
-#include "genhydro.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/topology/index.h"
-#include "fflibutil.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/genhydro.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/hizzie.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/specbond.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/xlate.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-
-#include "hizzie.h"
-#include "specbond.h"
-#include "xlate.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     char gmx[6];
diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index ec4f8927ce..8d9de45d32 100644
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -36,36 +36,35 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
-#include <math.h>
+#include "pdb2top.h"
+
 #include <ctype.h>
+#include <math.h>
+#include <stdio.h>
 
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
-#include "pdb2top.h"
-#include "gpp_nextnb.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "h_db.h"
-#include "pgutil.h"
-#include "resall.h"
-#include "topio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gen_ad.h"
 #include "gromacs/fileio/filenm.h"
-#include "gen_vsite.h"
-#include "add_par.h"
-#include "toputil.h"
-#include "fflibutil.h"
-#include "gromacs/legacyheaders/copyrite.h"
-
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gen_ad.h"
+#include "gromacs/gmxpreprocess/gen_vsite.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxpreprocess/pdb2top.h b/src/gromacs/gmxpreprocess/pdb2top.h
index 9b54d00197..cfbc800c87 100644
--- a/src/gromacs/gmxpreprocess/pdb2top.h
+++ b/src/gromacs/gmxpreprocess/pdb2top.h
@@ -38,11 +38,11 @@
 #ifndef GMX_GMXPREPROCESS_PDB2TOP_H
 #define GMX_GMXPREPROCESS_PDB2TOP_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
-#include "toputil.h"
-#include "hackblock.h"
 
 #ifdef __cplusplus
 extern "C"
diff --git a/src/gromacs/gmxpreprocess/pgutil.c b/src/gromacs/gmxpreprocess/pgutil.c
index 1cebc523b6..ff38d066ac 100644
--- a/src/gromacs/gmxpreprocess/pgutil.c
+++ b/src/gromacs/gmxpreprocess/pgutil.c
@@ -38,9 +38,11 @@
 
 #include "gmxpre.h"
 
-#include "gromacs/utility/cstringutil.h"
 #include "pgutil.h"
+
 #include <string.h>
+
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 
 #define BUFSIZE 1024
diff --git a/src/gromacs/gmxpreprocess/protonate.c b/src/gromacs/gmxpreprocess/protonate.c
index 5f1d99f6fc..4b73ff2760 100644
--- a/src/gromacs/gmxpreprocess/protonate.c
+++ b/src/gromacs/gmxpreprocess/protonate.c
@@ -39,20 +39,20 @@
 #include "protonate.h"
 
 #include <math.h>
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
+
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
-#include "genhydro.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/topology/index.h"
+#include "gromacs/gmxpreprocess/genhydro.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "hackblock.h"
-
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_protonate(int argc, char *argv[])
 {
diff --git a/src/gromacs/gmxpreprocess/read-conformation.cpp b/src/gromacs/gmxpreprocess/read-conformation.cpp
index b792b95c17..72886e8ced 100644
--- a/src/gromacs/gmxpreprocess/read-conformation.cpp
+++ b/src/gromacs/gmxpreprocess/read-conformation.cpp
@@ -37,8 +37,8 @@
 #include "read-conformation.h"
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/utility/cstringutil.h"
diff --git a/src/gromacs/gmxpreprocess/readadress.c b/src/gromacs/gmxpreprocess/readadress.c
index bc46c5802e..a95374cda8 100644
--- a/src/gromacs/gmxpreprocess/readadress.c
+++ b/src/gromacs/gmxpreprocess/readadress.c
@@ -38,7 +38,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "readir.h"
+#include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 0322b5b28c..8f55b6c660 100644
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -36,30 +36,30 @@
  */
 #include "gmxpre.h"
 
+#include "readir.h"
+
 #include <ctype.h>
 #include <limits.h>
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/warninp.h"
-#include "readir.h"
-#include "toputil.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/legacyheaders/inputrec.h"
-#include "calc_verletbuf.h"
-
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxpreprocess/readir.h b/src/gromacs/gmxpreprocess/readir.h
index eb93bbfc45..e20453e200 100644
--- a/src/gromacs/gmxpreprocess/readir.h
+++ b/src/gromacs/gmxpreprocess/readir.h
@@ -38,9 +38,9 @@
 #ifndef GMX_GMXPREPROCESS_READIR_H
 #define GMX_GMXPREPROCESS_READIR_H
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/legacyheaders/readinp.h"
-#include "grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/readpull.c b/src/gromacs/gmxpreprocess/readpull.c
index 70e484aae6..2e78022c5b 100644
--- a/src/gromacs/gmxpreprocess/readpull.c
+++ b/src/gromacs/gmxpreprocess/readpull.c
@@ -36,22 +36,22 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
 #include <stdlib.h>
+#include <string.h>
 
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "readir.h"
 #include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static char pulldim[STRLEN];
diff --git a/src/gromacs/gmxpreprocess/readrot.c b/src/gromacs/gmxpreprocess/readrot.c
index 527aca8764..f6289af803 100644
--- a/src/gromacs/gmxpreprocess/readrot.c
+++ b/src/gromacs/gmxpreprocess/readrot.c
@@ -36,15 +36,14 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "readir.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/trnio.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/txtdump.h"
-
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static char *RotStr = {"Enforced rotation:"};
 
diff --git a/src/gromacs/gmxpreprocess/resall.c b/src/gromacs/gmxpreprocess/resall.c
index b363023b1d..fe75e0cc65 100644
--- a/src/gromacs/gmxpreprocess/resall.c
+++ b/src/gromacs/gmxpreprocess/resall.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
+#include "resall.h"
+
 #include <ctype.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "resall.h"
-#include "pgutil.h"
-#include "fflibutil.h"
-
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/gmxpreprocess/resall.h b/src/gromacs/gmxpreprocess/resall.h
index c9bd68c60a..487ed643e2 100644
--- a/src/gromacs/gmxpreprocess/resall.h
+++ b/src/gromacs/gmxpreprocess/resall.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_RESALL_H
 #define GMX_GMXPREPROCESS_RESALL_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "hackblock.h"
-#include "gpp_atomtype.h"
-#include "grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/solvate.cpp b/src/gromacs/gmxpreprocess/solvate.cpp
index 421a49a207..5cfbe5d03e 100644
--- a/src/gromacs/gmxpreprocess/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/solvate.cpp
@@ -40,21 +40,20 @@
 
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/addconf.h"
+#include "gromacs/gmxpreprocess/read-conformation.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "addconf.h"
-#include "read-conformation.h"
-#include "gromacs/fileio/pdbio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #ifdef DEBUG
diff --git a/src/gromacs/gmxpreprocess/sortwater.c b/src/gromacs/gmxpreprocess/sortwater.c
index 43dcda6c5d..73c8b5472d 100644
--- a/src/gromacs/gmxpreprocess/sortwater.c
+++ b/src/gromacs/gmxpreprocess/sortwater.c
@@ -36,12 +36,12 @@
  */
 #include "gmxpre.h"
 
+#include "sortwater.h"
+
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "sortwater.h"
-
 #include "gromacs/random/random.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxpreprocess/specbond.c b/src/gromacs/gmxpreprocess/specbond.c
index 208092882b..2d1bfcf261 100644
--- a/src/gromacs/gmxpreprocess/specbond.c
+++ b/src/gromacs/gmxpreprocess/specbond.c
@@ -36,19 +36,20 @@
  */
 #include "gmxpre.h"
 
+#include "specbond.h"
+
 #include <ctype.h>
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
-#include "specbond.h"
-#include "pdb2top.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/macros.h"
 
 gmx_bool yesno(void)
 {
diff --git a/src/gromacs/gmxpreprocess/specbond.h b/src/gromacs/gmxpreprocess/specbond.h
index cd37ca9af3..4c8eedc307 100644
--- a/src/gromacs/gmxpreprocess/specbond.h
+++ b/src/gromacs/gmxpreprocess/specbond.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_SPECBOND_H
 #define GMX_GMXPREPROCESS_SPECBOND_H
 
-#include "pdb2top.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/ter_db.c b/src/gromacs/gmxpreprocess/ter_db.c
index 4817b27942..df0722c368 100644
--- a/src/gromacs/gmxpreprocess/ter_db.c
+++ b/src/gromacs/gmxpreprocess/ter_db.c
@@ -36,22 +36,22 @@
  */
 #include "gmxpre.h"
 
+#include "ter_db.h"
+
 #include <ctype.h>
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/futil.h"
-#include "resall.h"
-#include "h_db.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "ter_db.h"
-#include "toputil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "fflibutil.h"
-
-#include "gromacs/fileio/strdb.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* use bonded types definitions in hackblock.h */
 #define ekwRepl ebtsNR+1
diff --git a/src/gromacs/gmxpreprocess/ter_db.h b/src/gromacs/gmxpreprocess/ter_db.h
index 40547627da..45477d6207 100644
--- a/src/gromacs/gmxpreprocess/ter_db.h
+++ b/src/gromacs/gmxpreprocess/ter_db.h
@@ -38,8 +38,8 @@
 #ifndef GMX_GMXPREPROCESS_TER_DB_H
 #define GMX_GMXPREPROCESS_TER_DB_H
 
-#include "hackblock.h"
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp b/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
index 913208d7b5..b33d211ed4 100644
--- a/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
@@ -41,11 +41,13 @@
 
 #include "gmxpre.h"
 
-#include "../insert-molecules.h"
-#include "testutils/integrationtests.h"
-#include "testutils/cmdlinetest.h"
+#include "gromacs/gmxpreprocess/insert-molecules.h"
+
 #include "gromacs/utility/futil.h"
 
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
+
 namespace
 {
 
diff --git a/src/gromacs/gmxpreprocess/tests/solvate.cpp b/src/gromacs/gmxpreprocess/tests/solvate.cpp
index 947729b78e..86be31d271 100644
--- a/src/gromacs/gmxpreprocess/tests/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/tests/solvate.cpp
@@ -41,11 +41,13 @@
 
 #include "gmxpre.h"
 
-#include "../solvate.h"
-#include "testutils/integrationtests.h"
-#include "testutils/cmdlinetest.h"
+#include "gromacs/gmxpreprocess/solvate.h"
+
 #include "gromacs/utility/futil.h"
 
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
+
 namespace
 {
 
diff --git a/src/gromacs/gmxpreprocess/tomorse.c b/src/gromacs/gmxpreprocess/tomorse.c
index a326f16f0a..f1781e9043 100644
--- a/src/gromacs/gmxpreprocess/tomorse.c
+++ b/src/gromacs/gmxpreprocess/tomorse.c
@@ -37,21 +37,21 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "tomorse.h"
+
 #include <ctype.h>
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/cstringutil.h"
-#include "grompp-impl.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
-#include "toputil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gpp_atomtype.h"
-
-#include "tomorse.h"
 
 typedef struct {
     char *ai, *aj;
diff --git a/src/gromacs/gmxpreprocess/tomorse.h b/src/gromacs/gmxpreprocess/tomorse.h
index 39630fbf62..6a39ea6fd8 100644
--- a/src/gromacs/gmxpreprocess/tomorse.h
+++ b/src/gromacs/gmxpreprocess/tomorse.h
@@ -39,6 +39,7 @@
 #define GMX_GMXPREPROCESS_TOMORSE_H
 
 #include <stdio.h>
+
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/legacyheaders/typedefs.h"
diff --git a/src/gromacs/gmxpreprocess/topdirs.c b/src/gromacs/gmxpreprocess/topdirs.c
index d46b6922a8..1c42dfab2d 100644
--- a/src/gromacs/gmxpreprocess/topdirs.c
+++ b/src/gromacs/gmxpreprocess/topdirs.c
@@ -36,14 +36,15 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
+#include "topdirs.h"
+
 #include <stdarg.h>
+#include <stdio.h>
 
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "topdirs.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Must correspond to the directive enum in grompp-impl.h */
 static const char *directive_names[d_maxdir+1] = {
diff --git a/src/gromacs/gmxpreprocess/topdirs.h b/src/gromacs/gmxpreprocess/topdirs.h
index f619c8a4ea..fa62531eeb 100644
--- a/src/gromacs/gmxpreprocess/topdirs.h
+++ b/src/gromacs/gmxpreprocess/topdirs.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_TOPDIRS_H
 #define GMX_GMXPREPROCESS_TOPDIRS_H
 
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/topio.c b/src/gromacs/gmxpreprocess/topio.c
index f7efad094c..ffc95d0596 100644
--- a/src/gromacs/gmxpreprocess/topio.c
+++ b/src/gromacs/gmxpreprocess/topio.c
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "topio.h"
+
 #include <assert.h>
 #include <ctype.h>
 #include <errno.h>
@@ -46,34 +48,31 @@
 
 #include <sys/types.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/math/units.h"
+#include "gromacs/gmxpreprocess/gmxcpp.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/gmxpreprocess/topshake.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/warninp.h"
-#include "vsite_parm.h"
-
-#include "grompp-impl.h"
-#include "toputil.h"
-#include "toppush.h"
-#include "topdirs.h"
-#include "gpp_nextnb.h"
-#include "topio.h"
-#include "topshake.h"
-#include "gmxcpp.h"
-#include "gpp_bond_atomtype.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define OPENDIR     '[' /* starting sign for directive */
 #define CLOSEDIR    ']' /* ending sign for directive   */
diff --git a/src/gromacs/gmxpreprocess/topio.h b/src/gromacs/gmxpreprocess/topio.h
index 0767cef728..e03b102aa4 100644
--- a/src/gromacs/gmxpreprocess/topio.h
+++ b/src/gromacs/gmxpreprocess/topio.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_TOPIO_H
 #define GMX_GMXPREPROCESS_TOPIO_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "readir.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/toppush.c b/src/gromacs/gmxpreprocess/toppush.c
index fdefac9f14..161940b72e 100644
--- a/src/gromacs/gmxpreprocess/toppush.c
+++ b/src/gromacs/gmxpreprocess/toppush.c
@@ -36,21 +36,21 @@
  */
 #include "gmxpre.h"
 
+#include "toppush.h"
+
 #include <assert.h>
 #include <ctype.h>
 #include <math.h>
 #include <stdlib.h>
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "toputil.h"
-#include "toppush.h"
-#include "topdirs.h"
-#include "readir.h"
 #include "gromacs/legacyheaders/warninp.h"
-#include "gpp_atomtype.h"
-#include "gpp_bond_atomtype.h"
-
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/gmxpreprocess/toppush.h b/src/gromacs/gmxpreprocess/toppush.h
index 83526df792..1e14c57bc7 100644
--- a/src/gromacs/gmxpreprocess/toppush.h
+++ b/src/gromacs/gmxpreprocess/toppush.h
@@ -38,10 +38,10 @@
 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
 #define GMX_GMXPREPROCESS_TOPPUSH_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "toputil.h"
-#include "gpp_atomtype.h"
-#include "gpp_bond_atomtype.h"
 #include "gromacs/legacyheaders/warninp.h"
 
 #ifdef __cplusplus
diff --git a/src/gromacs/gmxpreprocess/topshake.c b/src/gromacs/gmxpreprocess/topshake.c
index 66a1036bdc..bd2662df2a 100644
--- a/src/gromacs/gmxpreprocess/topshake.c
+++ b/src/gromacs/gmxpreprocess/topshake.c
@@ -37,18 +37,19 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "topshake.h"
+
 #include <ctype.h>
 #include <math.h>
 
-#include "gromacs/math/units.h"
-#include "readir.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "topshake.h"
-#include "toppush.h"
-#include "toputil.h"
-#include "topdirs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/math/units.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void copy_bond (t_params *pr, int to, int from)
 /* copies an entry in a bond list to another position.
diff --git a/src/gromacs/gmxpreprocess/topshake.h b/src/gromacs/gmxpreprocess/topshake.h
index 2844b9f4dd..15e09da662 100644
--- a/src/gromacs/gmxpreprocess/topshake.h
+++ b/src/gromacs/gmxpreprocess/topshake.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_TOPSHAKE_H
 #define GMX_GMXPREPROCESS_TOPSHAKE_H
 
-#include "topio.h"
+#include "gromacs/gmxpreprocess/topio.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/toputil.c b/src/gromacs/gmxpreprocess/toputil.c
index a407b711df..ff567c8ea2 100644
--- a/src/gromacs/gmxpreprocess/toputil.c
+++ b/src/gromacs/gmxpreprocess/toputil.c
@@ -36,15 +36,15 @@
  */
 #include "gmxpre.h"
 
+#include "toputil.h"
+
 #include <assert.h>
 #include <math.h>
 #include <string.h>
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "gpp_atomtype.h"
-
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/gmxpreprocess/toputil.h b/src/gromacs/gmxpreprocess/toputil.h
index fd4259440b..d7d040effe 100644
--- a/src/gromacs/gmxpreprocess/toputil.h
+++ b/src/gromacs/gmxpreprocess/toputil.h
@@ -38,8 +38,8 @@
 #ifndef GMX_GMXPREPROCESS_TOPUTIL_H
 #define GMX_GMXPREPROCESS_TOPUTIL_H
 
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/vsite_parm.c b/src/gromacs/gmxpreprocess/vsite_parm.c
index edeab6fe4b..df9f9160ad 100644
--- a/src/gromacs/gmxpreprocess/vsite_parm.c
+++ b/src/gromacs/gmxpreprocess/vsite_parm.c
@@ -36,22 +36,23 @@
  */
 #include "gmxpre.h"
 
+#include "vsite_parm.h"
+
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "vsite_parm.h"
-#include "gromacs/utility/smalloc.h"
-#include "resall.h"
-#include "add_par.h"
-#include "gromacs/math/vec.h"
-#include "toputil.h"
-#include "gromacs/math/units.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     t_iatom a[4];
diff --git a/src/gromacs/gmxpreprocess/vsite_parm.h b/src/gromacs/gmxpreprocess/vsite_parm.h
index c127bbb88f..3001e74bc0 100644
--- a/src/gromacs/gmxpreprocess/vsite_parm.h
+++ b/src/gromacs/gmxpreprocess/vsite_parm.h
@@ -38,9 +38,9 @@
 #ifndef GMX_GMXPREPROCESS_VSITE_PARM_H
 #define GMX_GMXPREPROCESS_VSITE_PARM_H
 
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxpreprocess/x2top.c b/src/gromacs/gmxpreprocess/x2top.c
index f0ae9ad8d8..1dacc45c63 100644
--- a/src/gromacs/gmxpreprocess/x2top.c
+++ b/src/gromacs/gmxpreprocess/x2top.c
@@ -40,24 +40,23 @@
 
 #include <assert.h>
 
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxpreprocess/gen_ad.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/nm2type.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toppush.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/math/utilities.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/names.h"
-#include "toppush.h"
-#include "pdb2top.h"
-#include "gen_ad.h"
-#include "gpp_nextnb.h"
-#include "hackblock.h"
-#include "nm2type.h"
-
-#include "gromacs/bonded/bonded.h"
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/symtab.h"
diff --git a/src/gromacs/gmxpreprocess/xlate.c b/src/gromacs/gmxpreprocess/xlate.c
index d8dfc594f8..c4d2c7cfe2 100644
--- a/src/gromacs/gmxpreprocess/xlate.c
+++ b/src/gromacs/gmxpreprocess/xlate.c
@@ -36,15 +36,15 @@
  */
 #include "gmxpre.h"
 
+#include "xlate.h"
+
 #include <ctype.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "fflibutil.h"
-#include "hackblock.h"
-#include "xlate.h"
-
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
diff --git a/src/gromacs/imd/imd.c b/src/gromacs/imd/imd.c
index 7c6585260e..7c608c7bd5 100644
--- a/src/gromacs/imd/imd.c
+++ b/src/gromacs/imd/imd.c
@@ -49,11 +49,11 @@
 
 #include "imd.h"
 
+#include "config.h"
+
 #include <errno.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef GMX_NATIVE_WINDOWS
 #include <windows.h>
 #else
diff --git a/src/gromacs/imd/imd.h b/src/gromacs/imd/imd.h
index f6f26f2c3b..01aa585425 100644
--- a/src/gromacs/imd/imd.h
+++ b/src/gromacs/imd/imd.h
@@ -60,12 +60,12 @@
 #ifndef GMX_IMD_IMD_H
 #define GMX_IMD_IMD_H
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "../fileio/filenm.h"
-#include "../timing/wallcycle.h"
-
 #include "config.h"
 
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/timing/wallcycle.h"
+
 #ifdef GMX_NATIVE_WINDOWS
 #include <Windows.h>
 #define NOFLAGS 0
diff --git a/src/gromacs/imd/imdsocket.c b/src/gromacs/imd/imdsocket.c
index e322523845..ef70405d93 100644
--- a/src/gromacs/imd/imdsocket.c
+++ b/src/gromacs/imd/imdsocket.c
@@ -48,15 +48,16 @@
 
 #include "gmxpre.h"
 
+#include "imdsocket.h"
+
 #include "config.h"
 
 #include <errno.h>
 #include <string.h>
 
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/imd/imd.h"
 #include "gromacs/utility/fatalerror.h"
-#include "imdsocket.h"
-#include "imd.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_NATIVE_WINDOWS
 #ifdef GMX_HAVE_WINSOCK
diff --git a/src/gromacs/imd/imdsocket.h b/src/gromacs/imd/imdsocket.h
index d7f0ce9548..4effb0c76a 100644
--- a/src/gromacs/imd/imdsocket.h
+++ b/src/gromacs/imd/imdsocket.h
@@ -60,8 +60,8 @@
   #define GMX_IMD
   #endif
 #else
-#include <sys/socket.h>
 #include <netinet/in.h>
+#include <sys/socket.h>
 #define GMX_IMD
 #endif
 
diff --git a/src/gromacs/legacyheaders/bonded-threading.h b/src/gromacs/legacyheaders/bonded-threading.h
index f1ee5c88a5..e08765fa1f 100644
--- a/src/gromacs/legacyheaders/bonded-threading.h
+++ b/src/gromacs/legacyheaders/bonded-threading.h
@@ -38,7 +38,7 @@
 #ifndef GMX_LEGACYHEADERS_BONDED_THREADING_H
 #define GMX_LEGACYHEADERS_BONDED_THREADING_H
 
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/calcgrid.h b/src/gromacs/legacyheaders/calcgrid.h
index 1c6450387c..251b9e3d57 100644
--- a/src/gromacs/legacyheaders/calcgrid.h
+++ b/src/gromacs/legacyheaders/calcgrid.h
@@ -39,8 +39,8 @@
 
 #include <stdio.h>
 
-#include "../math/vectypes.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/calcmu.h b/src/gromacs/legacyheaders/calcmu.h
index f72bbfdb04..c9ed792d7b 100644
--- a/src/gromacs/legacyheaders/calcmu.h
+++ b/src/gromacs/legacyheaders/calcmu.h
@@ -39,8 +39,8 @@
 
 #include <stdio.h>
 
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/chargegroup.h b/src/gromacs/legacyheaders/chargegroup.h
index 417917fc65..26c81b081b 100644
--- a/src/gromacs/legacyheaders/chargegroup.h
+++ b/src/gromacs/legacyheaders/chargegroup.h
@@ -40,8 +40,8 @@
 
 #include <stdio.h>
 
-#include "../math/vectypes.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/checkpoint.h b/src/gromacs/legacyheaders/checkpoint.h
index 73ebd2a8f0..78f329dc23 100644
--- a/src/gromacs/legacyheaders/checkpoint.h
+++ b/src/gromacs/legacyheaders/checkpoint.h
@@ -39,9 +39,9 @@
 #define _checkpoint_h
 
 
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../fileio/gmxfio.h"
-#include "../fileio/filenm.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/coulomb.h b/src/gromacs/legacyheaders/coulomb.h
index 5c55f13f45..0b1f630408 100644
--- a/src/gromacs/legacyheaders/coulomb.h
+++ b/src/gromacs/legacyheaders/coulomb.h
@@ -39,6 +39,7 @@
 #define _coulomb_h
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
diff --git a/src/gromacs/legacyheaders/domdec.h b/src/gromacs/legacyheaders/domdec.h
index 2516c5b328..13b55711e8 100644
--- a/src/gromacs/legacyheaders/domdec.h
+++ b/src/gromacs/legacyheaders/domdec.h
@@ -36,11 +36,10 @@
 #ifndef _domdec_h
 #define _domdec_h
 
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/genborn.h"
-
-#include "../timing/wallcycle.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/ebin.h b/src/gromacs/legacyheaders/ebin.h
index 3dd6f42a05..f0bd0e7914 100644
--- a/src/gromacs/legacyheaders/ebin.h
+++ b/src/gromacs/legacyheaders/ebin.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/energy.h"
-#include "../fileio/enxio.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/force.h b/src/gromacs/legacyheaders/force.h
index 2bf5891d27..c93e720824 100644
--- a/src/gromacs/legacyheaders/force.h
+++ b/src/gromacs/legacyheaders/force.h
@@ -39,14 +39,13 @@
 #define _force_h
 
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/genborn.h"
-
-#include "../timing/wallcycle.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/gmx_omp_nthreads.h b/src/gromacs/legacyheaders/gmx_omp_nthreads.h
index c5ceef442e..1b7380fdb6 100644
--- a/src/gromacs/legacyheaders/gmx_omp_nthreads.h
+++ b/src/gromacs/legacyheaders/gmx_omp_nthreads.h
@@ -38,7 +38,7 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/gmx_thread_affinity.h b/src/gromacs/legacyheaders/gmx_thread_affinity.h
index dd10f54e56..d2a2ce2b55 100644
--- a/src/gromacs/legacyheaders/gmx_thread_affinity.h
+++ b/src/gromacs/legacyheaders/gmx_thread_affinity.h
@@ -38,7 +38,7 @@
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/types/hw_info.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/gpu_utils.h b/src/gromacs/legacyheaders/gpu_utils.h
index 27a44ee90e..08f596f404 100644
--- a/src/gromacs/legacyheaders/gpu_utils.h
+++ b/src/gromacs/legacyheaders/gpu_utils.h
@@ -40,8 +40,8 @@
 
 #include "config.h"
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef GMX_GPU
 #define FUNC_TERM_INT ;
diff --git a/src/gromacs/legacyheaders/main.h b/src/gromacs/legacyheaders/main.h
index 7dff7326be..43329b9d9a 100644
--- a/src/gromacs/legacyheaders/main.h
+++ b/src/gromacs/legacyheaders/main.h
@@ -40,9 +40,10 @@
 
 
 #include <stdio.h>
-#include "gromacs/legacyheaders/typedefs.h"
+
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/network.h"
-#include "../fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/md_support.h b/src/gromacs/legacyheaders/md_support.h
index 1fd51c4f9f..66f832310e 100644
--- a/src/gromacs/legacyheaders/md_support.h
+++ b/src/gromacs/legacyheaders/md_support.h
@@ -38,12 +38,11 @@
 #ifndef _md_support_h
 #define _md_support_h
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/globsig.h"
 #include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vcm.h"
-
-#include "../timing/wallcycle.h"
+#include "gromacs/legacyheaders/types/globsig.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/mdatoms.h b/src/gromacs/legacyheaders/mdatoms.h
index 54e4cb89cd..18d10ffb1f 100644
--- a/src/gromacs/legacyheaders/mdatoms.h
+++ b/src/gromacs/legacyheaders/mdatoms.h
@@ -42,8 +42,8 @@
 
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/mdebin.h b/src/gromacs/legacyheaders/mdebin.h
index 08d7b1f298..ef089de0ae 100644
--- a/src/gromacs/legacyheaders/mdebin.h
+++ b/src/gromacs/legacyheaders/mdebin.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/legacyheaders/ebin.h"
-#include "../fileio/enxio.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/state.h"
 
 #ifdef __cplusplus
diff --git a/src/gromacs/legacyheaders/mdrun.h b/src/gromacs/legacyheaders/mdrun.h
index e05b4ac11c..754a3796c3 100644
--- a/src/gromacs/legacyheaders/mdrun.h
+++ b/src/gromacs/legacyheaders/mdrun.h
@@ -40,19 +40,19 @@
 
 #include <stdio.h>
 #include <time.h>
-#include "gromacs/legacyheaders/typedefs.h"
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/sim_util.h"
 #include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/types/membedt.h"
 #include "gromacs/legacyheaders/types/globsig.h"
-
-#include "../fileio/filenm.h"
-#include "../timing/wallcycle.h"
+#include "gromacs/legacyheaders/types/membedt.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/network.h b/src/gromacs/legacyheaders/network.h
index 5e5e5f3d85..0824c6576a 100644
--- a/src/gromacs/legacyheaders/network.h
+++ b/src/gromacs/legacyheaders/network.h
@@ -45,8 +45,8 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
-#include "../utility/fatalerror.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/nonbonded.h b/src/gromacs/legacyheaders/nonbonded.h
index e61f1323f0..c985396e59 100644
--- a/src/gromacs/legacyheaders/nonbonded.h
+++ b/src/gromacs/legacyheaders/nonbonded.h
@@ -38,10 +38,10 @@
 #ifndef _nonbonded_h
 #define _nonbonded_h
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/ns.h b/src/gromacs/legacyheaders/ns.h
index a9d7202b55..26582e5d43 100644
--- a/src/gromacs/legacyheaders/ns.h
+++ b/src/gromacs/legacyheaders/ns.h
@@ -40,9 +40,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/oenv.h b/src/gromacs/legacyheaders/oenv.h
index d622c1b52b..ade929e081 100644
--- a/src/gromacs/legacyheaders/oenv.h
+++ b/src/gromacs/legacyheaders/oenv.h
@@ -38,8 +38,8 @@
 #ifndef _oenv_h
 #define _oenv_h
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/perf_est.h b/src/gromacs/legacyheaders/perf_est.h
index 4e548734fe..67b54dc46f 100644
--- a/src/gromacs/legacyheaders/perf_est.h
+++ b/src/gromacs/legacyheaders/perf_est.h
@@ -38,8 +38,8 @@
 #define _perf_est_h
 
 #include "gromacs/legacyheaders/types/inputrec.h"
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/pmalloc_cuda.h b/src/gromacs/legacyheaders/pmalloc_cuda.h
index 6b1be08a7f..d45890802c 100644
--- a/src/gromacs/legacyheaders/pmalloc_cuda.h
+++ b/src/gromacs/legacyheaders/pmalloc_cuda.h
@@ -39,6 +39,7 @@
 #include "config.h"
 
 #include <stdlib.h>
+
 #include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef GMX_GPU
diff --git a/src/gromacs/legacyheaders/pme.h b/src/gromacs/legacyheaders/pme.h
index 4001f52961..f71f6f51b2 100644
--- a/src/gromacs/legacyheaders/pme.h
+++ b/src/gromacs/legacyheaders/pme.h
@@ -39,11 +39,12 @@
 #define _pme_h
 
 #include <stdio.h>
+
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../math/gmxcomplex.h"
-#include "../timing/wallcycle.h"
-#include "../timing/walltime_accounting.h"
-#include "../legacyheaders/network.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/qmmm.h b/src/gromacs/legacyheaders/qmmm.h
index 3fc8e87f12..d3b5839f86 100644
--- a/src/gromacs/legacyheaders/qmmm.h
+++ b/src/gromacs/legacyheaders/qmmm.h
@@ -38,9 +38,9 @@
 #ifndef _QMMM_h
 #define _QMMM_h
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/rbin.h b/src/gromacs/legacyheaders/rbin.h
index ec2cd30dc6..fb0f7d6433 100644
--- a/src/gromacs/legacyheaders/rbin.h
+++ b/src/gromacs/legacyheaders/rbin.h
@@ -38,7 +38,7 @@
 #ifndef _rbin_h
 #define _rbin_h
 
-#include "../utility/real.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/readinp.h b/src/gromacs/legacyheaders/readinp.h
index 5d5044fa07..29b7a65bae 100644
--- a/src/gromacs/legacyheaders/readinp.h
+++ b/src/gromacs/legacyheaders/readinp.h
@@ -40,8 +40,8 @@
 
 #include <string.h>
 
-#include "../utility/basedefinitions.h"
 #include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/shellfc.h b/src/gromacs/legacyheaders/shellfc.h
index d16913544e..47f0d994c9 100644
--- a/src/gromacs/legacyheaders/shellfc.h
+++ b/src/gromacs/legacyheaders/shellfc.h
@@ -35,10 +35,9 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-#include "../timing/wallcycle.h"
-
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/sighandler.h b/src/gromacs/legacyheaders/sighandler.h
index 78edc547a9..b2531a67e9 100644
--- a/src/gromacs/legacyheaders/sighandler.h
+++ b/src/gromacs/legacyheaders/sighandler.h
@@ -40,7 +40,7 @@
 
 #include <signal.h>
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/sim_util.h b/src/gromacs/legacyheaders/sim_util.h
index b7f94dea7f..b1c89b790a 100644
--- a/src/gromacs/legacyheaders/sim_util.h
+++ b/src/gromacs/legacyheaders/sim_util.h
@@ -38,14 +38,14 @@
 #ifndef _sim_util_h
 #define _sim_util_h
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/mdoutf.h"
 #include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/vcm.h"
-#include "../fileio/enxio.h"
-#include "../fileio/mdoutf.h"
-#include "../timing/wallcycle.h"
-#include "../timing/walltime_accounting.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/splitter.h b/src/gromacs/legacyheaders/splitter.h
index 2e6bc8ec0f..7db0fcf5ac 100644
--- a/src/gromacs/legacyheaders/splitter.h
+++ b/src/gromacs/legacyheaders/splitter.h
@@ -40,7 +40,7 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/tables.h b/src/gromacs/legacyheaders/tables.h
index 56afdaa01d..a33250f446 100644
--- a/src/gromacs/legacyheaders/tables.h
+++ b/src/gromacs/legacyheaders/tables.h
@@ -35,8 +35,8 @@
 
 #ifndef _tables_h
 #define _tables_h
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/tgroup.h b/src/gromacs/legacyheaders/tgroup.h
index 5dacda4be9..64cc730fae 100644
--- a/src/gromacs/legacyheaders/tgroup.h
+++ b/src/gromacs/legacyheaders/tgroup.h
@@ -38,8 +38,8 @@
 #ifndef _tgroup_h
 #define _tgroup_h
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/txtdump.h b/src/gromacs/legacyheaders/txtdump.h
index 75116f7a5a..c8a3a086b8 100644
--- a/src/gromacs/legacyheaders/txtdump.h
+++ b/src/gromacs/legacyheaders/txtdump.h
@@ -40,8 +40,9 @@
 
 
 #include <stdio.h>
+
+#include "gromacs/fileio/tpxio.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../fileio/tpxio.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/typedefs.h b/src/gromacs/legacyheaders/typedefs.h
index aa2c698936..ad79e254bd 100644
--- a/src/gromacs/legacyheaders/typedefs.h
+++ b/src/gromacs/legacyheaders/typedefs.h
@@ -44,25 +44,25 @@
 
 #include <sys/types.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/types/enums.h"
-#include "../fileio/trx.h"
-#include "../topology/topology.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/constr.h"
 #include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
-#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/legacyheaders/types/nsgrid.h"
-#include "gromacs/legacyheaders/types/forcerec.h"
-#include "gromacs/legacyheaders/types/fcdata.h"
-#include "gromacs/legacyheaders/types/mdatom.h"
-#include "gromacs/legacyheaders/types/ifunc.h"
-#include "gromacs/legacyheaders/types/group.h"
-#include "gromacs/legacyheaders/types/state.h"
-#include "gromacs/legacyheaders/types/shellfc.h"
-#include "gromacs/legacyheaders/types/constr.h"
 #include "gromacs/legacyheaders/types/oenv.h"
-#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/topology/topology.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/types/commrec.h b/src/gromacs/legacyheaders/types/commrec.h
index 4fbb9bb882..4486c847b6 100644
--- a/src/gromacs/legacyheaders/types/commrec.h
+++ b/src/gromacs/legacyheaders/types/commrec.h
@@ -37,8 +37,8 @@
 #ifndef _commrec_h
 #define _commrec_h
 
-#include "../../utility/gmxmpi.h"
-#include "../typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/gmxmpi.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/types/forcerec.h b/src/gromacs/legacyheaders/types/forcerec.h
index 07fc2be29f..f3f1302d59 100644
--- a/src/gromacs/legacyheaders/types/forcerec.h
+++ b/src/gromacs/legacyheaders/types/forcerec.h
@@ -39,12 +39,12 @@
 #define GMX_LEGACYHEADERS_TYPES_FORCEREC_H
 
 #include "gromacs/legacyheaders/types/enums.h"
-#include "gromacs/legacyheaders/types/ns.h"
 #include "gromacs/legacyheaders/types/genborn.h"
-#include "gromacs/legacyheaders/types/qmmmrec.h"
-#include "../../topology/idef.h"
-#include "gromacs/legacyheaders/types/interaction_const.h"
 #include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/ns.h"
+#include "gromacs/legacyheaders/types/qmmmrec.h"
+#include "gromacs/topology/idef.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/types/hw_info.h b/src/gromacs/legacyheaders/types/hw_info.h
index 1ad1a771a1..13715add38 100644
--- a/src/gromacs/legacyheaders/types/hw_info.h
+++ b/src/gromacs/legacyheaders/types/hw_info.h
@@ -36,9 +36,9 @@
 #ifndef HWINFO_H
 #define HWINFO_H
 
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/gmx_cpuid.h"
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "../gmx_cpuid.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/types/ifunc.h b/src/gromacs/legacyheaders/types/ifunc.h
index 5b72be9154..25d13c6f58 100644
--- a/src/gromacs/legacyheaders/types/ifunc.h
+++ b/src/gromacs/legacyheaders/types/ifunc.h
@@ -39,9 +39,9 @@
 #ifndef _ifunc_h
 #define _ifunc_h
 
-#include "../../topology/idef.h"
-#include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/topology/idef.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/types/inputrec.h b/src/gromacs/legacyheaders/types/inputrec.h
index d6f7433ef8..26af01e0ef 100644
--- a/src/gromacs/legacyheaders/types/inputrec.h
+++ b/src/gromacs/legacyheaders/types/inputrec.h
@@ -39,9 +39,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/enums.h"
-#include "../../swap/enums.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/swap/enums.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/types/ns.h b/src/gromacs/legacyheaders/types/ns.h
index bc69cad31d..e141407525 100644
--- a/src/gromacs/legacyheaders/types/ns.h
+++ b/src/gromacs/legacyheaders/types/ns.h
@@ -38,8 +38,8 @@
 #ifndef GMX_LEGACYHEADERS_TYPES_NS_H
 #define GMX_LEGACYHEADERS_TYPES_NS_H
 
-#include "gromacs/legacyheaders/types/nsgrid.h"
 #include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/nsgrid.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/types/rgb.h b/src/gromacs/legacyheaders/types/rgb.h
index 60436a740f..f754da9231 100644
--- a/src/gromacs/legacyheaders/types/rgb.h
+++ b/src/gromacs/legacyheaders/types/rgb.h
@@ -37,7 +37,7 @@
 #ifndef GMX_LEGACYHEADERS_TYPES_RGB_H
 #define GMX_LEGACYHEADERS_TYPES_RGB_H
 
-#include "../../utility/real.h"
+#include "gromacs/utility/real.h"
 
 typedef struct {
     real r, g, b;
diff --git a/src/gromacs/legacyheaders/types/simple.h b/src/gromacs/legacyheaders/types/simple.h
index b648539ac8..ec8e23a860 100644
--- a/src/gromacs/legacyheaders/types/simple.h
+++ b/src/gromacs/legacyheaders/types/simple.h
@@ -37,9 +37,9 @@
 #ifndef _simple_h
 #define _simple_h
 
-#include "../../math/vectypes.h"
-#include "../../utility/basedefinitions.h"
-#include "../../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 typedef int         atom_id;      /* To indicate an atoms id         */
 #define NO_ATID     (atom_id)(~0) /* Use this to indicate invalid atid */
diff --git a/src/gromacs/legacyheaders/types/state.h b/src/gromacs/legacyheaders/types/state.h
index 76c2c1cc64..05b9135fe2 100644
--- a/src/gromacs/legacyheaders/types/state.h
+++ b/src/gromacs/legacyheaders/types/state.h
@@ -39,7 +39,7 @@
 
 
 #include "gromacs/legacyheaders/types/simple.h"
-#include "../../swap/enums.h"
+#include "gromacs/swap/enums.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/update.h b/src/gromacs/legacyheaders/update.h
index 55bfebdc2d..ce3e00d722 100644
--- a/src/gromacs/legacyheaders/update.h
+++ b/src/gromacs/legacyheaders/update.h
@@ -38,11 +38,10 @@
 #ifndef _update_h
 #define _update_h
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/network.h"
-
-#include "../timing/wallcycle.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/vcm.h b/src/gromacs/legacyheaders/vcm.h
index 0486b41f72..aaab02a806 100644
--- a/src/gromacs/legacyheaders/vcm.h
+++ b/src/gromacs/legacyheaders/vcm.h
@@ -42,9 +42,9 @@
 
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/viewit.h b/src/gromacs/legacyheaders/viewit.h
index af7fd882c0..e63616706a 100644
--- a/src/gromacs/legacyheaders/viewit.h
+++ b/src/gromacs/legacyheaders/viewit.h
@@ -38,8 +38,8 @@
 #ifndef _viewit_h
 #define _viewit_h
 
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/types/oenv.h"
-#include "../fileio/filenm.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/vsite.h b/src/gromacs/legacyheaders/vsite.h
index 79b6a839d6..6cbecbe391 100644
--- a/src/gromacs/legacyheaders/vsite.h
+++ b/src/gromacs/legacyheaders/vsite.h
@@ -41,7 +41,7 @@
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../pbcutil/ishift.h"
+#include "gromacs/pbcutil/ishift.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/legacyheaders/warninp.h b/src/gromacs/legacyheaders/warninp.h
index da485eda87..cd3f32c84a 100644
--- a/src/gromacs/legacyheaders/warninp.h
+++ b/src/gromacs/legacyheaders/warninp.h
@@ -38,7 +38,7 @@
 #ifndef _warninp_h
 #define _warninp_h
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/linearalgebra/eigensolver.c b/src/gromacs/linearalgebra/eigensolver.c
index 37e6bc7022..7d3f0d8754 100644
--- a/src/gromacs/linearalgebra/eigensolver.c
+++ b/src/gromacs/linearalgebra/eigensolver.c
@@ -43,8 +43,8 @@
 #include "gromacs/utility/real.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "gmx_lapack.h"
 #include "gmx_arpack.h"
+#include "gmx_lapack.h"
 
 void
 eigensolver(real *   a,
diff --git a/src/gromacs/linearalgebra/eigensolver.h b/src/gromacs/linearalgebra/eigensolver.h
index 0786bf55ce..0c2b97d92d 100644
--- a/src/gromacs/linearalgebra/eigensolver.h
+++ b/src/gromacs/linearalgebra/eigensolver.h
@@ -37,9 +37,8 @@
 #ifndef GMX_LINEARALGEBRA_EIGENSOLVER_H
 #define GMX_LINEARALGEBRA_EIGENSOLVER_H
 
-#include "../utility/real.h"
-
-#include "sparsematrix.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/linearalgebra/gmx_arpack.c b/src/gromacs/linearalgebra/gmx_arpack.c
index b7a424a733..287f0da282 100644
--- a/src/gromacs/linearalgebra/gmx_arpack.c
+++ b/src/gromacs/linearalgebra/gmx_arpack.c
@@ -35,13 +35,14 @@
  */
 #include "gmxpre.h"
 
+#include "gmx_arpack.h"
+
 #include <math.h>
 #include <string.h>
 
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
-#include "gmx_arpack.h"
 #include "gmx_blas.h"
 #include "gmx_lapack.h"
 
diff --git a/src/gromacs/linearalgebra/sparsematrix.c b/src/gromacs/linearalgebra/sparsematrix.c
index 34f5fd4443..5b2405c3de 100644
--- a/src/gromacs/linearalgebra/sparsematrix.c
+++ b/src/gromacs/linearalgebra/sparsematrix.c
@@ -39,8 +39,8 @@
 #include "sparsematrix.h"
 
 #include <assert.h>
-#include <stdlib.h>
 #include <stdio.h>
+#include <stdlib.h>
 
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/linearalgebra/sparsematrix.h b/src/gromacs/linearalgebra/sparsematrix.h
index d7b08f6dfb..04731f0181 100644
--- a/src/gromacs/linearalgebra/sparsematrix.h
+++ b/src/gromacs/linearalgebra/sparsematrix.h
@@ -39,8 +39,8 @@
 
 #include <stdio.h>
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/math/3dtransforms.cpp b/src/gromacs/math/3dtransforms.cpp
index b2247bdbfb..41e80d614f 100644
--- a/src/gromacs/math/3dtransforms.cpp
+++ b/src/gromacs/math/3dtransforms.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/math/3dtransforms.h"
+#include "3dtransforms.h"
 
 #include <math.h>
 #include <stdio.h>
diff --git a/src/gromacs/math/3dtransforms.h b/src/gromacs/math/3dtransforms.h
index 4bcba5c0fb..40516c60c6 100644
--- a/src/gromacs/math/3dtransforms.h
+++ b/src/gromacs/math/3dtransforms.h
@@ -39,8 +39,8 @@
 
 #include <stdio.h>
 
-#include "../utility/real.h"
-#include "vectypes.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/math/do_fit.h b/src/gromacs/math/do_fit.h
index f74bf1e895..7ccb652f19 100644
--- a/src/gromacs/math/do_fit.h
+++ b/src/gromacs/math/do_fit.h
@@ -37,10 +37,9 @@
 #ifndef GMX_MATH_DO_FIT_H
 #define GMX_MATH_DO_FIT_H
 
-#include "../legacyheaders/types/simple.h"
-#include "../utility/real.h"
-
-#include "vectypes.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/math/gmxcomplex.h b/src/gromacs/math/gmxcomplex.h
index 111ca37af1..8fa0c8ad6a 100644
--- a/src/gromacs/math/gmxcomplex.h
+++ b/src/gromacs/math/gmxcomplex.h
@@ -39,9 +39,8 @@
 
 #include <math.h>
 
-#include "../utility/real.h"
-
-#include "vectypes.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
 
 typedef struct {
     real re, im;
diff --git a/src/gromacs/math/units.h b/src/gromacs/math/units.h
index 4859f52e37..6afd10f2a9 100644
--- a/src/gromacs/math/units.h
+++ b/src/gromacs/math/units.h
@@ -43,7 +43,7 @@
  * be anywhere else in the code.
  */
 
-#include "utilities.h"
+#include "gromacs/math/utilities.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/math/utilities.c b/src/gromacs/math/utilities.c
index c2df23ec2e..03b7134427 100644
--- a/src/gromacs/math/utilities.c
+++ b/src/gromacs/math/utilities.c
@@ -38,12 +38,12 @@
 
 #include "utilities.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <limits.h>
 #include <math.h>
 
-#include "config.h"
-
 #ifdef HAVE__FINITE
 #include <float.h>
 #endif
diff --git a/src/gromacs/math/utilities.h b/src/gromacs/math/utilities.h
index 3ab1061140..2932220068 100644
--- a/src/gromacs/math/utilities.h
+++ b/src/gromacs/math/utilities.h
@@ -40,8 +40,8 @@
 #include <limits.h>
 #include <math.h>
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/math/vec.h b/src/gromacs/math/vec.h
index 2b2dcbc513..d5ee22cbe1 100644
--- a/src/gromacs/math/vec.h
+++ b/src/gromacs/math/vec.h
@@ -115,13 +115,12 @@
 
 #include <math.h>
 
-#include "units.h"
-#include "utilities.h"
-#include "vectypes.h"
-
-#include "../utility/basedefinitions.h"
-#include "../utility/fatalerror.h"
-#include "../utility/real.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/math/vectypes.h b/src/gromacs/math/vectypes.h
index fe9dd68194..ebb12dc512 100644
--- a/src/gromacs/math/vectypes.h
+++ b/src/gromacs/math/vectypes.h
@@ -37,7 +37,7 @@
 #ifndef GMX_MATH_VECTYPES_H
 #define GMX_MATH_VECTYPES_H
 
-#include "../utility/real.h"
+#include "gromacs/utility/real.h"
 
 #define XX      0 /* Defines for indexing in */
 #define YY      1 /* vectors                 */
diff --git a/src/gromacs/mdlib/adress.c b/src/gromacs/mdlib/adress.c
index dce59d513d..9e9db29089 100644
--- a/src/gromacs/mdlib/adress.c
+++ b/src/gromacs/mdlib/adress.c
@@ -37,12 +37,12 @@
 #include "gmxpre.h"
 
 #include "adress.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/types/simple.h"
+
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
 
 real
diff --git a/src/gromacs/mdlib/adress.h b/src/gromacs/mdlib/adress.h
index 7d3e9332f9..a25514d8b1 100644
--- a/src/gromacs/mdlib/adress.h
+++ b/src/gromacs/mdlib/adress.h
@@ -39,8 +39,8 @@
 #ifndef _adress_h_
 #define _adress_h_
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C"
diff --git a/src/gromacs/mdlib/calcmu.c b/src/gromacs/mdlib/calcmu.c
index 618b9cf0a2..7f2d383ca1 100644
--- a/src/gromacs/mdlib/calcmu.c
+++ b/src/gromacs/mdlib/calcmu.c
@@ -37,15 +37,16 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/calcmu.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/calcmu.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/math/vec.h"
 
 void calc_mu(int start, int homenr, rvec x[], real q[], real qB[],
              int nChargePerturbed,
diff --git a/src/gromacs/mdlib/calcvir.c b/src/gromacs/mdlib/calcvir.c
index 19d27411a1..0f6ab60aa0 100644
--- a/src/gromacs/mdlib/calcvir.c
+++ b/src/gromacs/mdlib/calcvir.c
@@ -39,7 +39,6 @@
 
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vectypes.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
diff --git a/src/gromacs/mdlib/clincs.c b/src/gromacs/mdlib/clincs.c
index 2b45442554..3423b0811a 100644
--- a/src/gromacs/mdlib/clincs.c
+++ b/src/gromacs/mdlib/clincs.c
@@ -40,20 +40,19 @@
 #include <math.h>
 #include <stdlib.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/constr.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/mdlib/constr.c b/src/gromacs/mdlib/constr.c
index 7b9addc389..fb075d4648 100644
--- a/src/gromacs/mdlib/constr.c
+++ b/src/gromacs/mdlib/constr.c
@@ -36,31 +36,31 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/constr.h"
+
 #include <assert.h>
 #include <stdlib.h>
 
+#include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/splitter.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/pulling/pull.h"
-
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/invblock.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/mdlib/coupling.c b/src/gromacs/mdlib/coupling.c
index 7583da1381..41806dc44b 100644
--- a/src/gromacs/mdlib/coupling.c
+++ b/src/gromacs/mdlib/coupling.c
@@ -38,20 +38,19 @@
 
 #include <assert.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/random/random.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #define NTROTTERPARTS 3
 
diff --git a/src/gromacs/mdlib/csettle.c b/src/gromacs/mdlib/csettle.c
index 44920009a9..bfd68b0aff 100644
--- a/src/gromacs/mdlib/csettle.c
+++ b/src/gromacs/mdlib/csettle.c
@@ -40,7 +40,6 @@
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/constr.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index 27d2bcb14a..bad4092e3e 100644
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -35,52 +35,52 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/domdec.h"
+
 #include "config.h"
 
-#include <stdio.h>
-#include <time.h>
+#include <assert.h>
 #include <math.h>
-#include <string.h>
+#include <stdio.h>
 #include <stdlib.h>
-#include <assert.h>
+#include <string.h>
+#include <time.h>
 
 #include "gromacs/bonded/bonded.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/domdec_network.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/bonded-threading.h"
 #include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/domdec_network.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/nsgrid.h"
-#include "gromacs/legacyheaders/shellfc.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "nbnxn_search.h"
-#include "gromacs/legacyheaders/bonded-threading.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/gpu_utils.h"
-
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/shellfc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/pulling/pull_rotation.h"
 #include "gromacs/swap/swapcoords.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/qsort_threadsafe.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/mdlib/domdec_box.c b/src/gromacs/mdlib/domdec_box.c
index 89fc97c820..7c9c4d088f 100644
--- a/src/gromacs/mdlib/domdec_box.c
+++ b/src/gromacs/mdlib/domdec_box.c
@@ -35,15 +35,14 @@
 
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/domdec_network.h"
-#include "gromacs/legacyheaders/nsgrid.h"
 #include "gromacs/legacyheaders/network.h"
-
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
 
 static void calc_cgcm_av_stddev(t_block *cgs, int n, rvec *x, rvec av, rvec stddev,
diff --git a/src/gromacs/mdlib/domdec_con.c b/src/gromacs/mdlib/domdec_con.c
index e83c16930e..e538a6a504 100644
--- a/src/gromacs/mdlib/domdec_con.c
+++ b/src/gromacs/mdlib/domdec_con.c
@@ -37,18 +37,17 @@
 
 #include <assert.h>
 
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/domdec_network.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/gmx_hash.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/mdlib/domdec_network.c b/src/gromacs/mdlib/domdec_network.c
index 8c1ef5153d..eec664a5d0 100644
--- a/src/gromacs/mdlib/domdec_network.c
+++ b/src/gromacs/mdlib/domdec_network.c
@@ -35,12 +35,13 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/domdec_network.h"
+
 #include "config.h"
 
 #include <string.h>
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/domdec_network.h"
 
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/gmxmpi.h"
 
 
diff --git a/src/gromacs/mdlib/domdec_setup.c b/src/gromacs/mdlib/domdec_setup.c
index 5caa68a9b5..0903c32d14 100644
--- a/src/gromacs/mdlib/domdec_setup.c
+++ b/src/gromacs/mdlib/domdec_setup.c
@@ -35,16 +35,17 @@
 
 #include "gmxpre.h"
 
-#include <stdio.h>
 #include <assert.h>
+#include <stdio.h>
+
 #include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/perf_est.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Margin for setting up the DD grid */
 #define DD_GRID_MARGIN_PRES_SCALE 1.05
diff --git a/src/gromacs/mdlib/domdec_top.c b/src/gromacs/mdlib/domdec_top.c
index 8360e45540..cf45ba3ff4 100644
--- a/src/gromacs/mdlib/domdec_top.c
+++ b/src/gromacs/mdlib/domdec_top.c
@@ -37,18 +37,17 @@
 
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/domdec_network.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
diff --git a/src/gromacs/mdlib/ebin.c b/src/gromacs/mdlib/ebin.c
index 33a0742130..8056f1f9bf 100644
--- a/src/gromacs/mdlib/ebin.c
+++ b/src/gromacs/mdlib/ebin.c
@@ -37,15 +37,17 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/ebin.h"
+
 #include <math.h>
 #include <string.h>
-#include "gromacs/utility/smalloc.h"
+
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/ebin.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 t_ebin *mk_ebin(void)
 {
diff --git a/src/gromacs/mdlib/ewald.c b/src/gromacs/mdlib/ewald.c
index bcf1865df3..97d0962f39 100644
--- a/src/gromacs/mdlib/ewald.c
+++ b/src/gromacs/mdlib/ewald.c
@@ -40,17 +40,16 @@
 #include <stdio.h>
 #include <stdlib.h>
 
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/utility/futil.h"
-#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/smalloc.h"
 
 #define TOL 2e-5
 
diff --git a/src/gromacs/mdlib/expanded.c b/src/gromacs/mdlib/expanded.c
index be1ea75c67..4996f51371 100644
--- a/src/gromacs/mdlib/expanded.c
+++ b/src/gromacs/mdlib/expanded.c
@@ -37,36 +37,34 @@
 #include <math.h>
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/calcmu.h"
 #include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/calcmu.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/xtcio.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 static void init_df_history_weights(df_history_t *dfhist, t_expanded *expand, int nlim)
 {
diff --git a/src/gromacs/mdlib/force.c b/src/gromacs/mdlib/force.c
index 03f4d9efd8..a4b3f65ec1 100644
--- a/src/gromacs/mdlib/force.c
+++ b/src/gromacs/mdlib/force.c
@@ -36,29 +36,29 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/force.h"
+
 #include "config.h"
 
 #include <assert.h>
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
diff --git a/src/gromacs/mdlib/forcerec.c b/src/gromacs/mdlib/forcerec.c
index 5be156dd7c..68edaad1c1 100644
--- a/src/gromacs/mdlib/forcerec.c
+++ b/src/gromacs/mdlib/forcerec.c
@@ -42,46 +42,43 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/tables.h"
-#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/gpu_utils.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/pmalloc_cuda.h"
 #include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/topology/mtop_util.h"
-#include "nbnxn_simd.h"
-#include "nbnxn_search.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_consts.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
-#include "gromacs/legacyheaders/inputrec.h"
-
+#include "gromacs/legacyheaders/tables.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "gromacs/legacyheaders/gpu_utils.h"
-#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-#include "gromacs/legacyheaders/pmalloc_cuda.h"
-#include "nb_verlet.h"
-
 t_forcerec *mk_forcerec(void)
 {
     t_forcerec *fr;
diff --git a/src/gromacs/mdlib/genborn.c b/src/gromacs/mdlib/genborn.c
index f3a8973262..c26de6a127 100644
--- a/src/gromacs/mdlib/genborn.c
+++ b/src/gromacs/mdlib/genborn.c
@@ -37,39 +37,39 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/genborn.h"
+
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/legacyheaders/nrnb.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
 #  ifdef GMX_DOUBLE
-#    include "genborn_sse2_double.h"
-#    include "genborn_allvsall_sse2_double.h"
+#    include "gromacs/mdlib/genborn_allvsall_sse2_double.h"
+#    include "gromacs/mdlib/genborn_sse2_double.h"
 #  else
-#    include "genborn_sse2_single.h"
-#    include "genborn_allvsall_sse2_single.h"
+#    include "gromacs/mdlib/genborn_allvsall_sse2_single.h"
+#    include "gromacs/mdlib/genborn_sse2_single.h"
 #  endif /* GMX_DOUBLE */
 #endif   /* SSE or AVX present */
 
-#include "genborn_allvsall.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
 
 /*#define DISABLE_SSE*/
 
diff --git a/src/gromacs/mdlib/genborn_allvsall.c b/src/gromacs/mdlib/genborn_allvsall.c
index b294cbbf5e..a18f2e1ac5 100644
--- a/src/gromacs/mdlib/genborn_allvsall.c
+++ b/src/gromacs/mdlib/genborn_allvsall.c
@@ -36,16 +36,16 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include "gromacs/legacyheaders/types/simple.h"
+#include "genborn_allvsall.h"
 
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
+#include <math.h>
 
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "genborn_allvsall.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
 
 
 typedef struct
diff --git a/src/gromacs/mdlib/genborn_allvsall.h b/src/gromacs/mdlib/genborn_allvsall.h
index 1f91757d16..83492bdef1 100644
--- a/src/gromacs/mdlib/genborn_allvsall.h
+++ b/src/gromacs/mdlib/genborn_allvsall.h
@@ -37,8 +37,8 @@
 #ifndef _GENBORN_ALLVSALL_H
 #define _GENBORN_ALLVSALL_H
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 int
 genborn_allvsall_calc_still_radii(t_forcerec *           fr,
diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_double.c b/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
index 4816c10133..5847525465 100644
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
@@ -37,15 +37,14 @@
 #include "gmxpre.h"
 
 #include <math.h>
-#include "gromacs/legacyheaders/types/simple.h"
-
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
 
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "genborn_allvsall.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
+#include "gromacs/utility/smalloc.h"
 
 
 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_double.h b/src/gromacs/mdlib/genborn_allvsall_sse2_double.h
index 045f5eb8a8..3629475dc3 100644
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_double.h
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_double.h
@@ -37,8 +37,8 @@
 #ifndef _GENBORN_ALLVSALL_SSE2_DOUBLE_H
 #define _GENBORN_ALLVSALL_SSE2_DOUBLE_H
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 int
 genborn_allvsall_calc_still_radii_sse2_double(t_forcerec *           fr,
diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_single.c b/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
index b574baea47..8c3ce47c99 100644
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
@@ -37,15 +37,14 @@
 #include "gmxpre.h"
 
 #include <math.h>
-#include "gromacs/legacyheaders/types/simple.h"
-
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
 
+#include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "genborn_allvsall.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
+#include "gromacs/utility/smalloc.h"
 
 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
 
diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_single.h b/src/gromacs/mdlib/genborn_allvsall_sse2_single.h
index 784b127a40..d1e908a985 100644
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_single.h
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_single.h
@@ -37,8 +37,8 @@
 #ifndef _GENBORN_ALLVSALL_SSE2_SINGLE_H
 #define _GENBORN_ALLVSALL_SSE2_SINGLE_H
 
-#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 int
 genborn_allvsall_calc_still_radii_sse2_single(t_forcerec *           fr,
diff --git a/src/gromacs/mdlib/genborn_sse2_double.c b/src/gromacs/mdlib/genborn_sse2_double.c
index 54eca2fe79..df68d0508e 100644
--- a/src/gromacs/mdlib/genborn_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_sse2_double.c
@@ -39,27 +39,25 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/genborn.h"
-
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Only compile this file if SSE2 intrinsics are available */
 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
-#include <gmx_sse2_double.h>
-#include <emmintrin.h>
-
 #include "genborn_sse2_double.h"
 
+#include <emmintrin.h>
+#include <gmx_sse2_double.h>
+
 int
 calc_gb_rad_still_sse2_double(t_commrec *cr, t_forcerec *fr,
                               int natoms, gmx_localtop_t *top,
diff --git a/src/gromacs/mdlib/genborn_sse2_single.c b/src/gromacs/mdlib/genborn_sse2_single.c
index bd5d6097dd..7c847473a1 100644
--- a/src/gromacs/mdlib/genborn_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_sse2_single.c
@@ -39,29 +39,27 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/genborn.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/genborn.h"
-
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* Only compile this file if SSE intrinsics are available */
 #if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
 
-#include <gmx_sse2_single.h>
-#include <emmintrin.h>
-
 #include "genborn_sse2_single.h"
 
+#include <emmintrin.h>
+#include <gmx_sse2_single.h>
+
 
 int
 calc_gb_rad_still_sse2_single(t_commrec *cr, t_forcerec *fr,
diff --git a/src/gromacs/mdlib/groupcoord.cpp b/src/gromacs/mdlib/groupcoord.cpp
index 17d3f713b1..b02f852374 100644
--- a/src/gromacs/mdlib/groupcoord.cpp
+++ b/src/gromacs/mdlib/groupcoord.cpp
@@ -37,11 +37,12 @@
 #include "gmxpre.h"
 
 #include "groupcoord.h"
+
+#include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
 
 #define MIN(a, b) (((a) < (b)) ? (a) : (b))
 
diff --git a/src/gromacs/mdlib/groupcoord.h b/src/gromacs/mdlib/groupcoord.h
index 4791aec83c..686ce17517 100644
--- a/src/gromacs/mdlib/groupcoord.h
+++ b/src/gromacs/mdlib/groupcoord.h
@@ -48,6 +48,7 @@
  */
 
 #include <stdio.h>
+
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 
diff --git a/src/gromacs/mdlib/init.c b/src/gromacs/mdlib/init.c
index 6b44531834..21549e2aa7 100644
--- a/src/gromacs/mdlib/init.c
+++ b/src/gromacs/mdlib/init.c
@@ -37,18 +37,19 @@
 #include "gmxpre.h"
 
 #include <stdio.h>
-#include "gromacs/legacyheaders/typedefs.h"
+
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/mvdata.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 #define BUFSIZE 256
 
diff --git a/src/gromacs/mdlib/iteratedconstraints.c b/src/gromacs/mdlib/iteratedconstraints.c
index a53633db6f..7899fdd12c 100644
--- a/src/gromacs/mdlib/iteratedconstraints.c
+++ b/src/gromacs/mdlib/iteratedconstraints.c
@@ -37,12 +37,13 @@
 #include "gmxpre.h"
 
 #include <math.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/md_support.h"
+
 #include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/iteratedconstraints.h"
+#include "gromacs/utility/fatalerror.h"
 
 #ifdef GMX_DOUBLE
 #define CONVERGEITER  0.000000001
diff --git a/src/gromacs/mdlib/md_support.cpp b/src/gromacs/mdlib/md_support.cpp
index 9e1abb9f1f..52b05bdd88 100644
--- a/src/gromacs/mdlib/md_support.cpp
+++ b/src/gromacs/mdlib/md_support.cpp
@@ -37,22 +37,22 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/md_support.h"
+
 #include <algorithm>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/mdlib/mdatom.c b/src/gromacs/mdlib/mdatom.c
index ea59275ec1..01c5c55bd6 100644
--- a/src/gromacs/mdlib/mdatom.c
+++ b/src/gromacs/mdlib/mdatom.c
@@ -38,12 +38,12 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/utility/smalloc.h"
 
 #define ALMOST_ZERO 1e-30
 
diff --git a/src/gromacs/mdlib/mdebin.c b/src/gromacs/mdlib/mdebin.c
index 84f24ac438..84b1db0f3d 100644
--- a/src/gromacs/mdlib/mdebin.c
+++ b/src/gromacs/mdlib/mdebin.c
@@ -36,28 +36,28 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/mdebin.h"
+
 #include <float.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/math/units.h"
 #include "gromacs/fileio/enxio.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/fileio/xvgr.h"
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/mdrun.h"
-#include "mdebin_bar.h"
-
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdebin_bar.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/smalloc.h"
 
 static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
diff --git a/src/gromacs/mdlib/mdebin_bar.c b/src/gromacs/mdlib/mdebin_bar.c
index a6bf3745ca..e351275864 100644
--- a/src/gromacs/mdlib/mdebin_bar.c
+++ b/src/gromacs/mdlib/mdebin_bar.c
@@ -36,16 +36,18 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
+#include "mdebin_bar.h"
+
 #include <float.h>
 #include <math.h>
+#include <string.h>
+
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "mdebin_bar.h"
 
 /* reset the delta_h list to prepare it for new values */
 static void mde_delta_h_reset(t_mde_delta_h *dh)
diff --git a/src/gromacs/mdlib/minimize.c b/src/gromacs/mdlib/minimize.c
index 00ebe44ee0..234bcbdd8f 100644
--- a/src/gromacs/mdlib/minimize.c
+++ b/src/gromacs/mdlib/minimize.c
@@ -42,35 +42,32 @@
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/bonded-threading.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/bonded-threading.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/md_logging.h"
-
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/mtxio.h"
-#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
 #include "gromacs/math/vec.h"
@@ -78,6 +75,7 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/mdlib/nb_verlet.h b/src/gromacs/mdlib/nb_verlet.h
index 78c4f691da..8fa19d0042 100644
--- a/src/gromacs/mdlib/nb_verlet.h
+++ b/src/gromacs/mdlib/nb_verlet.h
@@ -36,8 +36,8 @@
 #ifndef NB_VERLET_H
 #define NB_VERLET_H
 
-#include "nbnxn_pairlist.h"
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/mdlib/nbnxn_atomdata.c b/src/gromacs/mdlib/nbnxn_atomdata.c
index dd0e53d9c2..ca0f4999bc 100644
--- a/src/gromacs/mdlib/nbnxn_atomdata.c
+++ b/src/gromacs/mdlib/nbnxn_atomdata.c
@@ -35,6 +35,8 @@
 
 #include "gmxpre.h"
 
+#include "nbnxn_atomdata.h"
+
 #include "config.h"
 
 #include <assert.h>
@@ -42,16 +44,15 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "nbnxn_consts.h"
-#include "nbnxn_internal.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "thread_mpi/atomic.h"
 
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_internal.h"
+#include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
index 301627d872..799425edab 100644
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
@@ -36,11 +36,11 @@
 
 #include "nbnxn_cuda.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <stdlib.h>
 
-#include "config.h"
-
 #if defined(_MSVC)
 #include <limits>
 #endif
@@ -58,10 +58,11 @@
 #include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/cstringutil.h"
 
+#include "nbnxn_cuda_types.h"
+
 #if defined TEXOBJ_SUPPORTED && __CUDA_ARCH__ >= 300
 #define USE_TEXOBJ
 #endif
diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
index 6ccce27efd..174a9054af 100644
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
@@ -35,11 +35,11 @@
 #ifndef NBNXN_CUDA_H
 #define NBNXN_CUDA_H
 
+#include "config.h"
+
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
 #include "gromacs/legacyheaders/types/simple.h"
 
-#include "config.h"
-
 #ifdef GMX_GPU
 #define FUNC_TERM ;
 #else
diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
index fead7a37b4..f0e6fa8561 100644
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
@@ -34,36 +34,36 @@
  */
 #include "gmxpre.h"
 
+#include "nbnxn_cuda_data_mgmt.h"
+
 #include "config.h"
 
 #include <assert.h>
 #include <stdarg.h>
-#include <stdlib.h>
 #include <stdio.h>
+#include <stdlib.h>
 
 #include <cuda.h>
 
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gpu_utils.h"
+#include "gromacs/legacyheaders/pmalloc_cuda.h"
 #include "gromacs/legacyheaders/tables.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/enums.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/legacyheaders/types/interaction_const.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
-#include "../nbnxn_consts.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
-
-#include "nbnxn_cuda_types.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
-#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-#include "gromacs/legacyheaders/pmalloc_cuda.h"
-#include "gromacs/legacyheaders/gpu_utils.h"
-
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "nbnxn_cuda_types.h"
+
 static bool bUseCudaEventBlockingSync = false; /* makes the CPU thread block */
 
 /* This is a heuristically determined parameter for the Fermi architecture for
diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
index b3c34e9a44..00cac2ee45 100644
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
@@ -36,12 +36,12 @@
 #ifndef NBNXN_CUDA_DATA_MGMT_H
 #define NBNXN_CUDA_DATA_MGMT_H
 
-#include "gromacs/legacyheaders/types/simple.h"
+#include "config.h"
+
+#include "gromacs/legacyheaders/types/hw_info.h"
 #include "gromacs/legacyheaders/types/interaction_const.h"
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "gromacs/legacyheaders/types/hw_info.h"
-
-#include "config.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef GMX_GPU
 #define FUNC_TERM ;
diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh
index 7ea591db30..ac8a530f2c 100644
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh
@@ -38,7 +38,7 @@
  * code that is in double precision.
  */
 
-#include "../../gmxlib/cuda_tools/vectype_ops.cuh"
+#include "gromacs/gmxlib/cuda_tools/vectype_ops.cuh"
 
 #ifndef NBNXN_CUDA_KERNEL_UTILS_CUH
 #define NBNXN_CUDA_KERNEL_UTILS_CUH
diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh
index 897b956a74..c468306899 100644
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh
@@ -52,30 +52,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -88,30 +88,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -124,30 +124,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -161,30 +161,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -197,30 +197,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
@@ -233,30 +233,30 @@
 
 /* cut-off + V shift LJ */
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w geometric combination rules */
 #define LJ_EWALD_COMB_GEOM
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_GEOM
 #undef NB_KERNEL_FUNC_NAME
 /* LJ-Ewald w LB combination rules */
 #define LJ_EWALD_COMB_LB
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_EWALD_COMB_LB
 #undef NB_KERNEL_FUNC_NAME
 /* F switch LJ */
 #define LJ_FORCE_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_FORCE_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 /* V switch LJ */
 #define LJ_POT_SWITCH
 #define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
 #undef LJ_POT_SWITCH
 #undef NB_KERNEL_FUNC_NAME
 
diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h
index 367a59c75f..fe186eda89 100644
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h
@@ -46,10 +46,10 @@
 #ifndef NBNXN_CUDA_TYPES_H
 #define NBNXN_CUDA_TYPES_H
 
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
 #include "gromacs/legacyheaders/types/interaction_const.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
 
 /* CUDA versions from 5.0 above support texture objects. */
 #if CUDA_VERSION >= 5000
diff --git a/src/gromacs/mdlib/nbnxn_internal.h b/src/gromacs/mdlib/nbnxn_internal.h
index 5d5844cb22..909a4b07bb 100644
--- a/src/gromacs/mdlib/nbnxn_internal.h
+++ b/src/gromacs/mdlib/nbnxn_internal.h
@@ -36,11 +36,11 @@
 #ifndef _nbnxn_internal_h
 #define _nbnxn_internal_h
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "nbnxn_simd.h"
 #include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/timing/cyclecounter.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/timing/cyclecounter.h"
 
 
 /* Bounding box calculations are (currently) always in single precision, so
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
index ba8f2f0140..2fded68209 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.c
@@ -34,10 +34,10 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/pbcutil/ishift.h"
-
 #include "nbnxn_kernel_common.h"
 
+#include "gromacs/pbcutil/ishift.h"
+
 static void
 clear_f_all(const nbnxn_atomdata_t *nbat, real *f)
 {
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
index 01de457ba7..9432b2f311 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -37,7 +37,6 @@
 #include "config.h"
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
@@ -48,9 +47,10 @@
 {2}
 #define GMX_SIMD_J_UNROLL_SIZE {3}
 #include "{4}"
-#include "../nbnxn_kernel_common.h"
+
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre
index 1256eb6a6d..22ada3b193 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre
@@ -33,7 +33,6 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
index 30cfb49890..5e8ac7ca2a 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c
@@ -34,22 +34,21 @@
  */
 #include "gmxpre.h"
 
+#include "nbnxn_kernel_gpu_ref.h"
+
 #include "config.h"
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/force.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/ishift.h"
-
-#include "nbnxn_kernel_gpu_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
 #include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/pbcutil/ishift.h"
 
 #define NCL_PER_SUPERCL         (NBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER)
 #define CL_SIZE                 (NBNXN_GPU_CLUSTER_SIZE)
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
index efcafd3f1d..3db03bbec5 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
@@ -34,24 +34,23 @@
  */
 #include "gmxpre.h"
 
+#include "nbnxn_kernel_ref.h"
+
 #include "config.h"
 
-#include <math.h>
 #include <assert.h>
+#include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "nbnxn_kernel_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
-#include "gromacs/mdlib/nb_verlet.h"
-
 /*! \brief Typedefs for declaring lookup tables of kernel functions.
  */
 
@@ -74,21 +73,21 @@ typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
 /* Analytical reaction-field kernels */
 #define CALC_COUL_RF
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_POT_SWITCH
 #define LJ_EWALD
 #define LJ_CUT
 #define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_LB
 #undef LJ_CUT
 #undef LJ_EWALD
@@ -98,42 +97,42 @@ typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t     *nbl,
 /* Tabulated exclusion interaction electrostatics kernels */
 #define CALC_COUL_TAB
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_POT_SWITCH
 #define LJ_EWALD
 #define LJ_CUT
 #define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_LB
 #undef LJ_CUT
 #undef LJ_EWALD
 /* Twin-range cut-off kernels */
 #define VDW_CUTOFF_CHECK
 #define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_CUT
 #define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_FORCE_SWITCH
 #define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_POT_SWITCH
 #define LJ_EWALD
 #define LJ_CUT
 #define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_GEOM
 #define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
 #undef LJ_EWALD_COMB_LB
 #undef LJ_CUT
 #undef LJ_EWALD
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h
index 91447143a8..099a9079a4 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h
@@ -39,16 +39,16 @@
  */
 
 /* Include the force only kernels */
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
 
 /* Include the force+energy kernels */
 #define CALC_ENERGIES
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
 #undef CALC_ENERGIES
 
 /* Include the force+energygroups kernels */
 #define CALC_ENERGIES
 #define ENERGY_GROUPS
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
 #undef ENERGY_GROUPS
 #undef CALC_ENERGIES
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h
index cc6fb229b9..e0cfcef8bd 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h
@@ -332,19 +332,19 @@ NBK_FUNC_NAME(_VgrpF)
             {
 #define CALC_COULOMB
 #define HALF_LJ
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
 #undef HALF_LJ
 #undef CALC_COULOMB
             }
             else if (do_coul)
             {
 #define CALC_COULOMB
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
 #undef CALC_COULOMB
             }
             else
             {
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
             }
 #undef CHECK_EXCLS
             cjind++;
@@ -356,19 +356,19 @@ NBK_FUNC_NAME(_VgrpF)
             {
 #define CALC_COULOMB
 #define HALF_LJ
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
 #undef HALF_LJ
 #undef CALC_COULOMB
             }
             else if (do_coul)
             {
 #define CALC_COULOMB
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
 #undef CALC_COULOMB
             }
             else
             {
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
             }
         }
         ninner += cjind1 - cjind0;
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
index 5d081738f8..b5167b1fa8 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
@@ -35,10 +35,10 @@
 #ifndef _nbnxn_kernel_simd_utils_h_
 #define _nbnxn_kernel_simd_utils_h_
 
-#include "gromacs/legacyheaders/types/simple.h"
-
 #include "config.h"
 
+#include "gromacs/legacyheaders/types/simple.h"
+
 /*! \brief Provides hardware-specific utility routines for the SIMD kernels.
  *
  * Defines all functions, typedefs, constants and macros that have
@@ -65,7 +65,7 @@ prepare_table_load_buffer(const int gmx_unused *array)
     return NULL;
 }
 
-#include "nbnxn_kernel_simd_utils_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_ref.h"
 
 #else /* GMX_SIMD_REFERENCE */
 
@@ -96,17 +96,17 @@ prepare_table_load_buffer(int gmx_unused *array)
 
 #ifdef GMX_DOUBLE
 #if GMX_SIMD_REAL_WIDTH == 2
-#include "nbnxn_kernel_simd_utils_x86_128d.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128d.h"
 #else
-#include "nbnxn_kernel_simd_utils_x86_256d.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_256d.h"
 #endif
 #else /* GMX_DOUBLE */
 /* In single precision aligned FDV0 table loads are optimal */
 #define TAB_FDV0
 #if GMX_SIMD_REAL_WIDTH == 4
-#include "nbnxn_kernel_simd_utils_x86_128s.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h"
 #else
-#include "nbnxn_kernel_simd_utils_x86_256s.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_256s.h"
 #endif
 #endif /* GMX_DOUBLE */
 
@@ -125,11 +125,11 @@ static const int nbfp_stride = GMX_SIMD_REAL_WIDTH;
 #endif
 
 #ifdef GMX_SIMD_IBM_QPX
-#include "nbnxn_kernel_simd_utils_ibm_qpx.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_ibm_qpx.h"
 #endif /* GMX_SIMD_IBM_QPX */
 
 #ifdef __MIC__
-#include "nbnxn_kernel_simd_utils_x86_mic.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_mic.h"
 #endif
 
 #endif /* GMX_TARGET_X86 && !__MIC__ */
diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h
index 17d1186c48..589dafa320 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h
@@ -35,10 +35,10 @@
 #ifndef _nbnxn_kernel_simd_utils_x86_128s_h_
 #define _nbnxn_kernel_simd_utils_x86_128s_h_
 
-#include "gromacs/legacyheaders/types/simple.h"
-
 #include "config.h"
 
+#include "gromacs/legacyheaders/types/simple.h"
+
 /* This files contains all functions/macros for the SIMD kernels
  * which have explicit dependencies on the j-cluster size and/or SIMD-width.
  * The functionality which depends on the j-cluster size is:
diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
index 37ca75a469..ed1456873b 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -42,7 +42,6 @@
 #include "config.h"
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
@@ -57,9 +56,10 @@
 
 #define GMX_SIMD_J_UNROLL_SIZE 2
 #include "nbnxn_kernel_simd_2xnn.h"
-#include "../nbnxn_kernel_common.h"
+
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h
index 4e8235e1ac..f554134cbe 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h
@@ -38,7 +38,6 @@
  */
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
index a87ca0eb16..3f3abe8308 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
@@ -32,11 +32,11 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"
-#include "../../nbnxn_consts.h"
 #ifdef CALC_COUL_EWALD
 #include "gromacs/math/utilities.h"
 #endif
@@ -51,7 +51,7 @@
 /* The stride of all the atom data arrays is equal to half the SIMD width */
 #define STRIDE     UNROLLJ
 
-#include "../nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
 
 static gmx_inline void gmx_simdcall
 gmx_load_simd_2xnn_interactions(int                  excl,
diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h
index 590c09547d..21a63ab4aa 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h
@@ -603,13 +603,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
             }
 #undef HALF_LJ
 #undef CALC_COULOMB
@@ -621,13 +621,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
             }
 #undef CALC_COULOMB
         }
@@ -637,13 +637,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
             }
         }
 #undef CALC_LJ
diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
index be21910a62..d17ba1e7bd 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -42,7 +42,6 @@
 #include "config.h"
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
@@ -56,9 +55,10 @@
 
 #define GMX_SIMD_J_UNROLL_SIZE 1
 #include "nbnxn_kernel_simd_4xn.h"
-#include "../nbnxn_kernel_common.h"
+
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h
index c75d58a002..87c96994e8 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h
@@ -38,7 +38,6 @@
  */
 
 #include "gromacs/legacyheaders/typedefs.h"
-
 #include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 
diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
index 9216457430..146c95855b 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
@@ -32,11 +32,11 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"
-#include "../../nbnxn_consts.h"
 #ifdef CALC_COUL_EWALD
 #include "gromacs/math/utilities.h"
 #endif
@@ -57,7 +57,7 @@
 #define STRIDE     (UNROLLI)
 #endif
 
-#include "../nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
 
 static gmx_inline void gmx_simdcall
 gmx_load_simd_4xn_interactions(int gmx_unused             excl,
diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
index ffe53d5cd7..15bdf6ca91 100644
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
@@ -627,13 +627,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
             }
 #undef HALF_LJ
 #undef CALC_COULOMB
@@ -645,13 +645,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
             }
 #undef CALC_COULOMB
         }
@@ -661,13 +661,13 @@
 #define CHECK_EXCLS
             while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
                 cjind++;
             }
 #undef CHECK_EXCLS
             for (; (cjind < cjind1); cjind++)
             {
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
             }
         }
 #undef CALC_LJ
diff --git a/src/gromacs/mdlib/nbnxn_pairlist.h b/src/gromacs/mdlib/nbnxn_pairlist.h
index fa03d2681b..3f441ad16c 100644
--- a/src/gromacs/mdlib/nbnxn_pairlist.h
+++ b/src/gromacs/mdlib/nbnxn_pairlist.h
@@ -37,6 +37,7 @@
 #define _nbnxn_pairlist_h
 
 #include "thread_mpi/atomic.h"
+
 #include "gromacs/legacyheaders/types/nblist.h"
 
 #ifdef __cplusplus
diff --git a/src/gromacs/mdlib/nbnxn_search.c b/src/gromacs/mdlib/nbnxn_search.c
index 6c1e301a07..f13de8c7db 100644
--- a/src/gromacs/mdlib/nbnxn_search.c
+++ b/src/gromacs/mdlib/nbnxn_search.c
@@ -37,6 +37,8 @@
 
 #include "nbnxn_search.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 #include <string.h>
@@ -55,8 +57,6 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "config.h"
-
 /* nbnxn_internal.h included gromacs/simd/macros.h */
 #include "gromacs/mdlib/nbnxn_internal.h"
 #ifdef GMX_SIMD
diff --git a/src/gromacs/mdlib/nbnxn_search.h b/src/gromacs/mdlib/nbnxn_search.h
index 7c7def3ff4..8e644bf21a 100644
--- a/src/gromacs/mdlib/nbnxn_search.h
+++ b/src/gromacs/mdlib/nbnxn_search.h
@@ -37,7 +37,7 @@
 #define _nbnxn_search_h
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/mdlib/nbnxn_search_simd_2xnn.h b/src/gromacs/mdlib/nbnxn_search_simd_2xnn.h
index 59760f4b94..2ff7bc991e 100644
--- a/src/gromacs/mdlib/nbnxn_search_simd_2xnn.h
+++ b/src/gromacs/mdlib/nbnxn_search_simd_2xnn.h
@@ -34,7 +34,7 @@
  */
 
 /* Get the half-width SIMD stuff from the kernel utils files */
-#include "nbnxn_kernels/nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
 
 
 #if GMX_SIMD_REAL_WIDTH >= 2*NBNXN_CPU_CLUSTER_I_SIZE
diff --git a/src/gromacs/mdlib/nlistheuristics.c b/src/gromacs/mdlib/nlistheuristics.c
index abe5815555..44f789e7bb 100644
--- a/src/gromacs/mdlib/nlistheuristics.c
+++ b/src/gromacs/mdlib/nlistheuristics.c
@@ -38,7 +38,6 @@
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/nlistheuristics.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c
index 8eb8a70d62..9145929c47 100644
--- a/src/gromacs/mdlib/ns.c
+++ b/src/gromacs/mdlib/ns.c
@@ -36,32 +36,32 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/ns.h"
+
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nsgrid.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/topology/mtop_util.h"
-
-#include "gromacs/legacyheaders/domdec.h"
-#include "adress.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "adress.h"
+
 /*
  *    E X C L U S I O N   H A N D L I N G
  */
diff --git a/src/gromacs/mdlib/nsgrid.c b/src/gromacs/mdlib/nsgrid.c
index 8ad27efc6c..0f0120e0e1 100644
--- a/src/gromacs/mdlib/nsgrid.c
+++ b/src/gromacs/mdlib/nsgrid.c
@@ -37,21 +37,22 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/nsgrid.h"
+
+#include <stdio.h>
 #include <stdlib.h>
 
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/nsgrid.h"
-#include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include <stdio.h>
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
+#include "gromacs/utility/smalloc.h"
 
 /***********************************
  *         Grid Routines
diff --git a/src/gromacs/mdlib/perf_est.c b/src/gromacs/mdlib/perf_est.c
index 29010b067a..837113f2ae 100644
--- a/src/gromacs/mdlib/perf_est.c
+++ b/src/gromacs/mdlib/perf_est.c
@@ -36,17 +36,17 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/perf_est.h"
+
 #include <math.h>
 
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 
-#include "gromacs/legacyheaders/perf_est.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "nbnxn_search.h"
-#include "nbnxn_consts.h"
-
 /* Computational cost of bonded, non-bonded and PME calculations.
  * This will be machine dependent.
  * The numbers here are accurate for Intel Core2 and AMD Athlon 64
diff --git a/src/gromacs/mdlib/pme.c b/src/gromacs/mdlib/pme.c
index 284480184e..67a12ab58d 100644
--- a/src/gromacs/mdlib/pme.c
+++ b/src/gromacs/mdlib/pme.c
@@ -59,6 +59,8 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/pme.h"
+
 #include "config.h"
 
 #include <assert.h>
@@ -67,27 +69,25 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fft/parallel_3dfft.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/legacyheaders/coulomb.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/macros.h"
-
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/fft/parallel_3dfft.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
 #include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/timing/cyclecounter.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
 
 /* Include the SIMD macro file and then check for support */
 #include "gromacs/simd/simd.h"
@@ -1436,7 +1436,7 @@ static void spread_coefficients_bsplines_thread(pmegrid_t                    *pm
 #define PME_SPREAD_SIMD4_ALIGNED
 #define PME_ORDER 4
 #endif
-#include "pme_simd4.h"
+#include "gromacs/mdlib/pme_simd4.h"
 #else
                     DO_BSPLINE(4);
 #endif
@@ -1445,7 +1445,7 @@ static void spread_coefficients_bsplines_thread(pmegrid_t                    *pm
 #ifdef PME_SIMD4_SPREAD_GATHER
 #define PME_SPREAD_SIMD4_ALIGNED
 #define PME_ORDER 5
-#include "pme_simd4.h"
+#include "gromacs/mdlib/pme_simd4.h"
 #else
                     DO_BSPLINE(5);
 #endif
@@ -2599,7 +2599,7 @@ static void gather_f_bsplines(gmx_pme_t pme, real *grid,
 #define PME_GATHER_F_SIMD4_ALIGNED
 #define PME_ORDER 4
 #endif
-#include "pme_simd4.h"
+#include "gromacs/mdlib/pme_simd4.h"
 #else
                     DO_FSPLINE(4);
 #endif
@@ -2608,7 +2608,7 @@ static void gather_f_bsplines(gmx_pme_t pme, real *grid,
 #ifdef PME_SIMD4_SPREAD_GATHER
 #define PME_GATHER_F_SIMD4_ALIGNED
 #define PME_ORDER 5
-#include "pme_simd4.h"
+#include "gromacs/mdlib/pme_simd4.h"
 #else
                     DO_FSPLINE(5);
 #endif
diff --git a/src/gromacs/mdlib/pme_pp.c b/src/gromacs/mdlib/pme_pp.c
index 6ed1d563fb..f00d242ae7 100644
--- a/src/gromacs/mdlib/pme_pp.c
+++ b/src/gromacs/mdlib/pme_pp.c
@@ -39,21 +39,20 @@
 
 #include "config.h"
 
-
+#include <math.h>
 #include <stdio.h>
 #include <string.h>
-#include <math.h>
+
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/sighandler.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/sighandler.h"
-
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 enum {
     eCommType_ChargeA, eCommType_ChargeB, eCommType_SQRTC6A, eCommType_SQRTC6B,
diff --git a/src/gromacs/mdlib/qm_gamess.c b/src/gromacs/mdlib/qm_gamess.c
index 9fcaed86dc..d913f7f489 100644
--- a/src/gromacs/mdlib/qm_gamess.c
+++ b/src/gromacs/mdlib/qm_gamess.c
@@ -45,20 +45,20 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* QMMM sub routines */
diff --git a/src/gromacs/mdlib/qm_gaussian.c b/src/gromacs/mdlib/qm_gaussian.c
index 1092a65046..6339b94f8a 100644
--- a/src/gromacs/mdlib/qm_gaussian.c
+++ b/src/gromacs/mdlib/qm_gaussian.c
@@ -45,20 +45,20 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* TODO: this should be made thread-safe */
diff --git a/src/gromacs/mdlib/qm_mopac.c b/src/gromacs/mdlib/qm_mopac.c
index 7f1bea8a83..6eb689cd3e 100644
--- a/src/gromacs/mdlib/qm_mopac.c
+++ b/src/gromacs/mdlib/qm_mopac.c
@@ -45,20 +45,20 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* mopac interface routines */
diff --git a/src/gromacs/mdlib/qm_orca.c b/src/gromacs/mdlib/qm_orca.c
index f5f85e4f8d..11ddfd325b 100644
--- a/src/gromacs/mdlib/qm_orca.c
+++ b/src/gromacs/mdlib/qm_orca.c
@@ -41,20 +41,20 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 /* ORCA interface routines */
 
diff --git a/src/gromacs/mdlib/qmmm.c b/src/gromacs/mdlib/qmmm.c
index ccb566ae9c..bb83405a55 100644
--- a/src/gromacs/mdlib/qmmm.c
+++ b/src/gromacs/mdlib/qmmm.c
@@ -36,6 +36,8 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/qmmm.h"
+
 #include "config.h"
 
 #include <math.h>
@@ -43,25 +45,21 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/force.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/topology/mtop_util.h"
-
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/mdlib/rf_util.c b/src/gromacs/mdlib/rf_util.c
index ee68bd8ee0..a4703cca24 100644
--- a/src/gromacs/mdlib/rf_util.c
+++ b/src/gromacs/mdlib/rf_util.c
@@ -36,16 +36,15 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/copyrite.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
 
 real RF_excl_correction(const t_forcerec *fr, t_graph *g,
                         const t_mdatoms *mdatoms, const t_blocka *excl,
diff --git a/src/gromacs/mdlib/shakef.c b/src/gromacs/mdlib/shakef.c
index fba6074500..7ee7dbe2a8 100644
--- a/src/gromacs/mdlib/shakef.c
+++ b/src/gromacs/mdlib/shakef.c
@@ -38,12 +38,12 @@
 
 #include <math.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct gmx_shakedata
 {
diff --git a/src/gromacs/mdlib/shellfc.c b/src/gromacs/mdlib/shellfc.c
index ad3f4d5c6e..ce00047a38 100644
--- a/src/gromacs/mdlib/shellfc.c
+++ b/src/gromacs/mdlib/shellfc.c
@@ -36,29 +36,29 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/shellfc.h"
+
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/shellfc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/mdlib/sim_util.c b/src/gromacs/mdlib/sim_util.c
index 4090760008..886f6acdd3 100644
--- a/src/gromacs/mdlib/sim_util.c
+++ b/src/gromacs/mdlib/sim_util.c
@@ -38,13 +38,13 @@
 
 #include "gromacs/legacyheaders/sim_util.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
@@ -78,7 +78,6 @@
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/mdlib/adress.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_atomdata.h"
 #include "gromacs/mdlib/nbnxn_search.h"
@@ -99,6 +98,8 @@
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "adress.h"
+
 void print_time(FILE                     *out,
                 gmx_walltime_accounting_t walltime_accounting,
                 gmx_int64_t               step,
diff --git a/src/gromacs/mdlib/stat.c b/src/gromacs/mdlib/stat.c
index e0d2ee19c6..280237f215 100644
--- a/src/gromacs/mdlib/stat.c
+++ b/src/gromacs/mdlib/stat.c
@@ -36,32 +36,32 @@
  */
 #include "gmxpre.h"
 
-#include <string.h>
 #include <stdio.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/rbin.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/fileio/xtcio.h"
+#include <string.h>
+
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/trnio.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/fileio/xtcio.h"
 #include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/rbin.h"
 #include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct gmx_global_stat
 {
diff --git a/src/gromacs/mdlib/tables.c b/src/gromacs/mdlib/tables.c
index 5f5d9d58fd..1c3389e493 100644
--- a/src/gromacs/mdlib/tables.c
+++ b/src/gromacs/mdlib/tables.c
@@ -36,21 +36,23 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/tables.h"
+
 #include <math.h>
-#include "gromacs/math/utilities.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
+
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/units.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/tables.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* All the possible (implemented) table functions */
 enum {
diff --git a/src/gromacs/mdlib/tgroup.c b/src/gromacs/mdlib/tgroup.c
index db9a9bb988..1baec82abd 100644
--- a/src/gromacs/mdlib/tgroup.c
+++ b/src/gromacs/mdlib/tgroup.c
@@ -37,17 +37,19 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/tgroup.h"
+
 #include <math.h>
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/math/vec.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/rbin.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
 {
diff --git a/src/gromacs/mdlib/tpi.c b/src/gromacs/mdlib/tpi.c
index 39ebeaf237..7da23c74c3 100644
--- a/src/gromacs/mdlib/tpi.c
+++ b/src/gromacs/mdlib/tpi.c
@@ -41,40 +41,38 @@
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
 #include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/random/random.h"
-#include "gromacs/math/units.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void global_max(t_commrec *cr, int *n)
 {
diff --git a/src/gromacs/mdlib/update.c b/src/gromacs/mdlib/update.c
index 68c30a18e2..3be84a8a93 100644
--- a/src/gromacs/mdlib/update.c
+++ b/src/gromacs/mdlib/update.c
@@ -36,31 +36,31 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
+#include "gromacs/legacyheaders/update.h"
+
 #include <math.h>
+#include <stdio.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/random/random.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/legacyheaders/constr.h"
 #include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
+#include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxomp.h"
diff --git a/src/gromacs/mdlib/vcm.c b/src/gromacs/mdlib/vcm.c
index c6d3b2a310..31c2cf2c94 100644
--- a/src/gromacs/mdlib/vcm.c
+++ b/src/gromacs/mdlib/vcm.c
@@ -37,14 +37,15 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
+
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/smalloc.h"
 
 t_vcm *init_vcm(FILE *fp, gmx_groups_t *groups, t_inputrec *ir)
 {
diff --git a/src/gromacs/mdlib/vsite.c b/src/gromacs/mdlib/vsite.c
index a9df773ec2..984426f319 100644
--- a/src/gromacs/mdlib/vsite.c
+++ b/src/gromacs/mdlib/vsite.c
@@ -36,22 +36,22 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/vsite.h"
+
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/mdlib/wall.c b/src/gromacs/mdlib/wall.c
index 38f26e3c1c..bdc5c90e40 100644
--- a/src/gromacs/mdlib/wall.c
+++ b/src/gromacs/mdlib/wall.c
@@ -40,14 +40,13 @@
 #include <math.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/math/vec.h"
-
-#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/mdlib/wnblist.c b/src/gromacs/mdlib/wnblist.c
index 62aa867b6b..afcef8db51 100644
--- a/src/gromacs/mdlib/wnblist.c
+++ b/src/gromacs/mdlib/wnblist.c
@@ -39,17 +39,18 @@
 
 #include <stdio.h>
 #include <string.h>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/smalloc.h"
 
 #define header "Neighborlist:"
 
diff --git a/src/gromacs/onlinehelp/helpformat.h b/src/gromacs/onlinehelp/helpformat.h
index 6891adfb08..98df196f44 100644
--- a/src/gromacs/onlinehelp/helpformat.h
+++ b/src/gromacs/onlinehelp/helpformat.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@
 
 #include <string>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/onlinehelp/helpmanager.h b/src/gromacs/onlinehelp/helpmanager.h
index 122d72242e..4418edf871 100644
--- a/src/gromacs/onlinehelp/helpmanager.h
+++ b/src/gromacs/onlinehelp/helpmanager.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@
 
 #include <string>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/onlinehelp/helptopic.h b/src/gromacs/onlinehelp/helptopic.h
index f67bc8e993..bff75e3876 100644
--- a/src/gromacs/onlinehelp/helptopic.h
+++ b/src/gromacs/onlinehelp/helptopic.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -44,11 +44,10 @@
 #ifndef GMX_ONLINEHELP_HELPTOPIC_H
 #define GMX_ONLINEHELP_HELPTOPIC_H
 
-#include "../utility/common.h"
-#include "../utility/stringutil.h"
-#include "../utility/uniqueptr.h"
-
-#include "helptopicinterface.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/uniqueptr.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/onlinehelp/helptopicinterface.h b/src/gromacs/onlinehelp/helptopicinterface.h
index e3f0c92d44..2a6479ed27 100644
--- a/src/gromacs/onlinehelp/helptopicinterface.h
+++ b/src/gromacs/onlinehelp/helptopicinterface.h
@@ -56,7 +56,7 @@
 #ifndef GMX_ONLINEHELP_HELPTOPICINTERFACE_H
 #define GMX_ONLINEHELP_HELPTOPICINTERFACE_H
 
-#include "../utility/uniqueptr.h"
+#include "gromacs/utility/uniqueptr.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/onlinehelp/helpwritercontext.h b/src/gromacs/onlinehelp/helpwritercontext.h
index 157ea00b8a..8bbc2b63e8 100644
--- a/src/gromacs/onlinehelp/helpwritercontext.h
+++ b/src/gromacs/onlinehelp/helpwritercontext.h
@@ -46,7 +46,7 @@
 #include <string>
 #include <vector>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/onlinehelp/tests/helpformat.cpp b/src/gromacs/onlinehelp/tests/helpformat.cpp
index f74a80da34..797593e6b8 100644
--- a/src/gromacs/onlinehelp/tests/helpformat.cpp
+++ b/src/gromacs/onlinehelp/tests/helpformat.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/onlinehelp/helpformat.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/stringtest.h"
 
 namespace
diff --git a/src/gromacs/options.h b/src/gromacs/options.h
index 4b11e1f7c0..a6bc7e8362 100644
--- a/src/gromacs/options.h
+++ b/src/gromacs/options.h
@@ -146,10 +146,10 @@
 #ifndef GMX_OPTIONS_H
 #define GMX_OPTIONS_H
 
-#include "fileio/filenm.h"
-#include "options/basicoptions.h"
-#include "options/filenameoption.h"
-#include "options/filenameoptionmanager.h"
-#include "options/options.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/filenameoptionmanager.h"
+#include "gromacs/options/options.h"
 
 #endif
diff --git a/src/gromacs/options/abstractoption.cpp b/src/gromacs/options/abstractoption.cpp
index c81d0e2a56..a71ed24353 100644
--- a/src/gromacs/options/abstractoption.cpp
+++ b/src/gromacs/options/abstractoption.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/abstractoption.h"
+#include "abstractoption.h"
 
 #include "gromacs/options/abstractoptionstorage.h"
 #include "gromacs/options/optionflags.h"
diff --git a/src/gromacs/options/abstractoption.h b/src/gromacs/options/abstractoption.h
index 1152081eca..2793f2f0fa 100644
--- a/src/gromacs/options/abstractoption.h
+++ b/src/gromacs/options/abstractoption.h
@@ -57,9 +57,8 @@
 #include <string>
 #include <vector>
 
-#include "../utility/common.h"
-
-#include "optionflags.h"
+#include "gromacs/options/optionflags.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/abstractoptionstorage.h b/src/gromacs/options/abstractoptionstorage.h
index 9cb9ff543e..9081d03898 100644
--- a/src/gromacs/options/abstractoptionstorage.h
+++ b/src/gromacs/options/abstractoptionstorage.h
@@ -45,9 +45,8 @@
 
 #include <string>
 
-#include "../utility/common.h"
-
-#include "optionflags.h"
+#include "gromacs/options/optionflags.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/basicoptions.cpp b/src/gromacs/options/basicoptions.cpp
index 8dff27360d..4124555607 100644
--- a/src/gromacs/options/basicoptions.cpp
+++ b/src/gromacs/options/basicoptions.cpp
@@ -42,7 +42,6 @@
 #include "gmxpre.h"
 
 #include "basicoptions.h"
-#include "basicoptionstorage.h"
 
 #include <cerrno>
 #include <cstdio>
@@ -56,6 +55,8 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "basicoptionstorage.h"
+
 namespace
 {
 
diff --git a/src/gromacs/options/basicoptions.h b/src/gromacs/options/basicoptions.h
index 67f14e31d9..4d58fcf241 100644
--- a/src/gromacs/options/basicoptions.h
+++ b/src/gromacs/options/basicoptions.h
@@ -48,10 +48,9 @@
 
 #include <string>
 
-#include "../utility/basedefinitions.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/basicoptionstorage.h b/src/gromacs/options/basicoptionstorage.h
index 823ec97beb..59ab9f16fc 100644
--- a/src/gromacs/options/basicoptionstorage.h
+++ b/src/gromacs/options/basicoptionstorage.h
@@ -45,8 +45,8 @@
 #include <string>
 #include <vector>
 
-#include "basicoptions.h"
-#include "optionstoragetemplate.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/optionstoragetemplate.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/filenameoption.cpp b/src/gromacs/options/filenameoption.cpp
index 171c668a5a..1f13641786 100644
--- a/src/gromacs/options/filenameoption.cpp
+++ b/src/gromacs/options/filenameoption.cpp
@@ -42,7 +42,6 @@
 #include "gmxpre.h"
 
 #include "filenameoption.h"
-#include "filenameoptionstorage.h"
 
 #include <cstring>
 
@@ -57,6 +56,8 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "filenameoptionstorage.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/options/filenameoption.h b/src/gromacs/options/filenameoption.h
index 479a35834a..2c1536fc8c 100644
--- a/src/gromacs/options/filenameoption.h
+++ b/src/gromacs/options/filenameoption.h
@@ -46,8 +46,8 @@
 #include <string>
 #include <vector>
 
-#include "abstractoption.h"
-#include "optionfiletype.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/optionfiletype.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/filenameoptionmanager.h b/src/gromacs/options/filenameoptionmanager.h
index 1c492e1970..0fd50ceec8 100644
--- a/src/gromacs/options/filenameoptionmanager.h
+++ b/src/gromacs/options/filenameoptionmanager.h
@@ -45,9 +45,8 @@
 
 #include <string>
 
-#include "options.h"
-
-#include "../utility/common.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/filenameoptionstorage.h b/src/gromacs/options/filenameoptionstorage.h
index 84a0f8fc21..7628a379d1 100644
--- a/src/gromacs/options/filenameoptionstorage.h
+++ b/src/gromacs/options/filenameoptionstorage.h
@@ -45,9 +45,9 @@
 #include <string>
 #include <vector>
 
-#include "filenameoption.h"
-#include "optionfiletype.h"
-#include "optionstoragetemplate.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/optionfiletype.h"
+#include "gromacs/options/optionstoragetemplate.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/optionflags.h b/src/gromacs/options/optionflags.h
index 5a4ff6399b..9157ecba9d 100644
--- a/src/gromacs/options/optionflags.h
+++ b/src/gromacs/options/optionflags.h
@@ -46,7 +46,7 @@
 #ifndef GMX_OPTIONS_OPTIONFLAGS_H
 #define GMX_OPTIONS_OPTIONFLAGS_H
 
-#include "../utility/flags.h"
+#include "gromacs/utility/flags.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/options-impl.h b/src/gromacs/options/options-impl.h
index ce23aad952..3fba6da02a 100644
--- a/src/gromacs/options/options-impl.h
+++ b/src/gromacs/options/options-impl.h
@@ -45,9 +45,9 @@
 #include <string>
 #include <vector>
 
-#include "abstractoption.h"
-#include "optionmanagercontainer.h"
-#include "options.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/optionmanagercontainer.h"
+#include "gromacs/options/options.h"
 #include "gromacs/utility/uniqueptr.h"
 
 namespace gmx
diff --git a/src/gromacs/options/options.cpp b/src/gromacs/options/options.cpp
index 9aa05a27ff..aec42fc98f 100644
--- a/src/gromacs/options/options.cpp
+++ b/src/gromacs/options/options.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/options.h"
+#include "options.h"
 
 #include "gromacs/options/abstractoption.h"
 #include "gromacs/options/abstractoptionstorage.h"
diff --git a/src/gromacs/options/options.h b/src/gromacs/options/options.h
index 7623086796..6c6c51fcfd 100644
--- a/src/gromacs/options/options.h
+++ b/src/gromacs/options/options.h
@@ -48,10 +48,9 @@
 
 #include <string>
 
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/optionsassigner.cpp b/src/gromacs/options/optionsassigner.cpp
index 6274213a55..df3f1320d8 100644
--- a/src/gromacs/options/optionsassigner.cpp
+++ b/src/gromacs/options/optionsassigner.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/optionsassigner.h"
+#include "optionsassigner.h"
 
 #include <deque>
 
diff --git a/src/gromacs/options/optionsassigner.h b/src/gromacs/options/optionsassigner.h
index 5047b180dc..d56529e707 100644
--- a/src/gromacs/options/optionsassigner.h
+++ b/src/gromacs/options/optionsassigner.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,7 +47,7 @@
 
 #include <string>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/optionstoragetemplate.h b/src/gromacs/options/optionstoragetemplate.h
index dae027c79a..ad00611d04 100644
--- a/src/gromacs/options/optionstoragetemplate.h
+++ b/src/gromacs/options/optionstoragetemplate.h
@@ -48,12 +48,11 @@
 
 #include <boost/scoped_ptr.hpp>
 
-#include "../utility/common.h"
-#include "../utility/exceptions.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
-#include "abstractoptionstorage.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/optionsvisitor.cpp b/src/gromacs/options/optionsvisitor.cpp
index 9f74f946d6..814ae734fd 100644
--- a/src/gromacs/options/optionsvisitor.cpp
+++ b/src/gromacs/options/optionsvisitor.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/optionsvisitor.h"
+#include "optionsvisitor.h"
 
 #include "gromacs/options/abstractoptionstorage.h"
 #include "gromacs/options/options.h"
diff --git a/src/gromacs/options/optionsvisitor.h b/src/gromacs/options/optionsvisitor.h
index 862b28ee57..934efb97fb 100644
--- a/src/gromacs/options/optionsvisitor.h
+++ b/src/gromacs/options/optionsvisitor.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,9 +47,8 @@
 
 #include <string>
 
-#include "../utility/common.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/options/tests/abstractoptionstorage.cpp b/src/gromacs/options/tests/abstractoptionstorage.cpp
index cdd5bbaf1b..1682129575 100644
--- a/src/gromacs/options/tests/abstractoptionstorage.cpp
+++ b/src/gromacs/options/tests/abstractoptionstorage.cpp
@@ -44,16 +44,16 @@
  */
 #include "gmxpre.h"
 
-#include <vector>
 #include <string>
+#include <vector>
 
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
 #include "gromacs/options/abstractoption.h"
 #include "gromacs/options/options.h"
-#include "gromacs/options/optionstoragetemplate.h"
 #include "gromacs/options/optionsassigner.h"
+#include "gromacs/options/optionstoragetemplate.h"
 #include "gromacs/utility/exceptions.h"
 
 #include "testutils/testasserts.h"
diff --git a/src/gromacs/options/tests/option.cpp b/src/gromacs/options/tests/option.cpp
index 2cc756bc94..70b513bdb7 100644
--- a/src/gromacs/options/tests/option.cpp
+++ b/src/gromacs/options/tests/option.cpp
@@ -44,8 +44,8 @@
  */
 #include "gmxpre.h"
 
-#include <vector>
 #include <string>
+#include <vector>
 
 #include <gtest/gtest.h>
 
diff --git a/src/gromacs/options/tests/optionsassigner.cpp b/src/gromacs/options/tests/optionsassigner.cpp
index 9b6e244c0a..cf9648cc1c 100644
--- a/src/gromacs/options/tests/optionsassigner.cpp
+++ b/src/gromacs/options/tests/optionsassigner.cpp
@@ -47,6 +47,8 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/options/optionsassigner.h"
+
 #include <limits>
 #include <vector>
 
@@ -54,7 +56,6 @@
 
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
-#include "gromacs/options/optionsassigner.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"
 
diff --git a/src/gromacs/options/tests/timeunitmanager.cpp b/src/gromacs/options/tests/timeunitmanager.cpp
index 11989bc002..9e5f57fd18 100644
--- a/src/gromacs/options/tests/timeunitmanager.cpp
+++ b/src/gromacs/options/tests/timeunitmanager.cpp
@@ -43,12 +43,13 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/options/timeunitmanager.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/optionsassigner.h"
-#include "gromacs/options/timeunitmanager.h"
 
 #include "testutils/testasserts.h"
 
diff --git a/src/gromacs/options/timeunitmanager.cpp b/src/gromacs/options/timeunitmanager.cpp
index d77e10700c..b687c31bb7 100644
--- a/src/gromacs/options/timeunitmanager.cpp
+++ b/src/gromacs/options/timeunitmanager.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/options/timeunitmanager.h"
+#include "timeunitmanager.h"
 
 #include <cstdlib>
 
diff --git a/src/gromacs/options/timeunitmanager.h b/src/gromacs/options/timeunitmanager.h
index 7ad7fe3243..76e08312be 100644
--- a/src/gromacs/options/timeunitmanager.h
+++ b/src/gromacs/options/timeunitmanager.h
@@ -43,7 +43,7 @@
 #ifndef GMX_OPTIONS_TIMEUNITMANAGER_H
 #define GMX_OPTIONS_TIMEUNITMANAGER_H
 
-#include "../utility/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/pbcutil/mshift.cpp b/src/gromacs/pbcutil/mshift.cpp
index fa47a80e1a..346f029ead 100644
--- a/src/gromacs/pbcutil/mshift.cpp
+++ b/src/gromacs/pbcutil/mshift.cpp
@@ -36,14 +36,13 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/pbcutil/mshift.h"
+#include "mshift.h"
 
 #include <string.h>
 
 #include <algorithm>
 
 #include "gromacs/legacyheaders/types/ifunc.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/pbcutil/pbc.c b/src/gromacs/pbcutil/pbc.c
index cfdc3be419..e6d4c49230 100644
--- a/src/gromacs/pbcutil/pbc.c
+++ b/src/gromacs/pbcutil/pbc.c
@@ -36,18 +36,17 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/pbcutil/pbc.h"
+#include "pbc.h"
 
 #include <assert.h>
 #include <math.h>
 
-#include "gromacs/legacyheaders/types/inputrec.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/ishift.h"
diff --git a/src/gromacs/pbcutil/pbc.h b/src/gromacs/pbcutil/pbc.h
index 8fa140d8f0..8fc7b68224 100644
--- a/src/gromacs/pbcutil/pbc.h
+++ b/src/gromacs/pbcutil/pbc.h
@@ -39,11 +39,11 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/commrec_fwd.h"
-#include "../legacyheaders/types/inputrec.h"
-#include "../math/vectypes.h"
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/pbcutil/rmpbc.c b/src/gromacs/pbcutil/rmpbc.c
index 09f10c043c..4d91ac4783 100644
--- a/src/gromacs/pbcutil/rmpbc.c
+++ b/src/gromacs/pbcutil/rmpbc.c
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/pbcutil/rmpbc.h"
+#include "rmpbc.h"
 
 #include "gromacs/fileio/trx.h"
 #include "gromacs/math/vec.h"
@@ -44,8 +44,8 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/idef.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 typedef struct {
diff --git a/src/gromacs/pbcutil/rmpbc.h b/src/gromacs/pbcutil/rmpbc.h
index 3f90bdb265..ff9107a7d2 100644
--- a/src/gromacs/pbcutil/rmpbc.h
+++ b/src/gromacs/pbcutil/rmpbc.h
@@ -37,7 +37,7 @@
 #ifndef GMX_PBCUTIL_RMPBC_H
 #define GMX_PBCUTIL_RMPBC_H
 
-#include "../math/vectypes.h"
+#include "gromacs/math/vectypes.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/pulling/pull.c b/src/gromacs/pulling/pull.c
index e84ad19714..575e07ca87 100644
--- a/src/gromacs/pulling/pull.c
+++ b/src/gromacs/pulling/pull.c
@@ -36,28 +36,28 @@
  */
 #include "gmxpre.h"
 
+#include "pull.h"
+
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "pull.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static void pull_print_group_x(FILE *out, ivec dim, const t_pull_group *pgrp)
diff --git a/src/gromacs/pulling/pull.h b/src/gromacs/pulling/pull.h
index d8362c5353..3a5f8d6b57 100644
--- a/src/gromacs/pulling/pull.h
+++ b/src/gromacs/pulling/pull.h
@@ -50,8 +50,8 @@
 #ifndef GMX_PULLING_PULL_H
 #define GMX_PULLING_PULL_H
 
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "../fileio/filenm.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/pulling/pull_rotation.c b/src/gromacs/pulling/pull_rotation.c
index 0aa84dbcce..dd74b44df5 100644
--- a/src/gromacs/pulling/pull_rotation.c
+++ b/src/gromacs/pulling/pull_rotation.c
@@ -36,37 +36,36 @@
  */
 #include "gmxpre.h"
 
+#include "pull_rotation.h"
+
 #include "config.h"
 
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/cyclecounter.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/qsort_threadsafe.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/utility/smalloc.h"
 
 static char *RotStr = {"Enforced rotation:"};
 
diff --git a/src/gromacs/pulling/pull_rotation.h b/src/gromacs/pulling/pull_rotation.h
index 567b4e95c8..28d380195b 100644
--- a/src/gromacs/pulling/pull_rotation.h
+++ b/src/gromacs/pulling/pull_rotation.h
@@ -48,9 +48,9 @@
 #ifndef GMX_PULLING_PULL_ROTATION_H
 #define GMX_PULLING_PULL_ROTATION_H
 
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/timing/wallcycle.h"
-#include "../fileio/filenm.h"
 
 
 #ifdef __cplusplus
diff --git a/src/gromacs/pulling/pullutil.c b/src/gromacs/pulling/pullutil.c
index 57bc3401c5..53072c1ef2 100644
--- a/src/gromacs/pulling/pullutil.c
+++ b/src/gromacs/pulling/pullutil.c
@@ -38,19 +38,19 @@
 
 #include <stdlib.h>
 
-#include "gromacs/utility/futil.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "pull.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
                              rvec *x,
diff --git a/src/gromacs/random/random.c b/src/gromacs/random/random.c
index 9150e64f3e..b8295a73d7 100644
--- a/src/gromacs/random/random.c
+++ b/src/gromacs/random/random.c
@@ -38,13 +38,13 @@
 
 #include "random.h"
 
+#include "config.h"
+
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <time.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
@@ -52,11 +52,11 @@
 #include <process.h>
 #endif
 
+#include "external/Random123-1.08/include/Random123/threefry.h"
+
 #include "gromacs/math/utilities.h"
 #include "gromacs/random/random_gausstable.h"
 
-#include "external/Random123-1.08/include/Random123/threefry.h"
-
 #define RNG_N 624
 #define RNG_M 397
 #define RNG_MATRIX_A 0x9908b0dfUL   /* constant vector a */
diff --git a/src/gromacs/selection.h b/src/gromacs/selection.h
index 0588ce36aa..ef47702a21 100644
--- a/src/gromacs/selection.h
+++ b/src/gromacs/selection.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -81,9 +81,9 @@
 #ifndef GMX_SELECTION_H
 #define GMX_SELECTION_H
 
-#include "selection/selection.h"
-#include "selection/selectioncollection.h"
-#include "selection/selectionoption.h"
-#include "selection/selectionoptionmanager.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/selection/selectionoptionmanager.h"
 
 #endif
diff --git a/src/gromacs/selection/centerofmass.cpp b/src/gromacs/selection/centerofmass.cpp
index a3fa6c369a..474175ef89 100644
--- a/src/gromacs/selection/centerofmass.cpp
+++ b/src/gromacs/selection/centerofmass.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/selection/centerofmass.h"
+#include "centerofmass.h"
 
 #include <errno.h>
 
diff --git a/src/gromacs/selection/centerofmass.h b/src/gromacs/selection/centerofmass.h
index 494d39b26e..4aa7cf8288 100644
--- a/src/gromacs/selection/centerofmass.h
+++ b/src/gromacs/selection/centerofmass.h
@@ -74,8 +74,8 @@
 #ifndef GMX_SELECTION_CENTEROFMASS_H
 #define GMX_SELECTION_CENTEROFMASS_H
 
-#include "../legacyheaders/types/simple.h"
-#include "../math/vectypes.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vectypes.h"
 
 struct t_block;
 struct t_blocka;
diff --git a/src/gromacs/selection/compiler.cpp b/src/gromacs/selection/compiler.cpp
index 293073fd50..4b696a29ae 100644
--- a/src/gromacs/selection/compiler.cpp
+++ b/src/gromacs/selection/compiler.cpp
@@ -273,16 +273,14 @@
 
 #include "compiler.h"
 
-#include <algorithm>
-
 #include <math.h>
 #include <stdarg.h>
 
+#include <algorithm>
+
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
@@ -290,8 +288,10 @@
 #include "evaluate.h"
 #include "keywords.h"
 #include "mempool.h"
+#include "poscalc.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 using std::min;
 using gmx::SelectionTreeElement;
diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp
index 1a38971544..dd3d3d1de5 100644
--- a/src/gromacs/selection/evaluate.cpp
+++ b/src/gromacs/selection/evaluate.cpp
@@ -52,22 +52,23 @@
  */
 #include "gmxpre.h"
 
+#include "evaluate.h"
+
 #include <string.h>
 
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "evaluate.h"
 #include "mempool.h"
+#include "poscalc.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 using gmx::SelectionTreeElement;
 using gmx::SelectionTreeElementPointer;
diff --git a/src/gromacs/selection/indexutil.cpp b/src/gromacs/selection/indexutil.cpp
index 6fd4666a01..a38fe36205 100644
--- a/src/gromacs/selection/indexutil.cpp
+++ b/src/gromacs/selection/indexutil.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/selection/indexutil.h"
+#include "indexutil.h"
 
 #include <cstdlib>
 #include <cstring>
diff --git a/src/gromacs/selection/indexutil.h b/src/gromacs/selection/indexutil.h
index bdbaaf0076..dbfe7e77cf 100644
--- a/src/gromacs/selection/indexutil.h
+++ b/src/gromacs/selection/indexutil.h
@@ -65,8 +65,8 @@
 
 #include <string>
 
-#include "../legacyheaders/types/simple.h"
-#include "../topology/block.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/topology/block.h"
 
 struct t_topology;
 
diff --git a/src/gromacs/selection/mempool.cpp b/src/gromacs/selection/mempool.cpp
index 99dd91dba6..675932440f 100644
--- a/src/gromacs/selection/mempool.cpp
+++ b/src/gromacs/selection/mempool.cpp
@@ -41,6 +41,8 @@
  */
 #include "gmxpre.h"
 
+#include "mempool.h"
+
 #include <stdlib.h>
 
 #include <new>
@@ -50,8 +52,6 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "mempool.h"
-
 //! Alignment in bytes for all returned blocks.
 #define ALIGN_STEP 8
 
diff --git a/src/gromacs/selection/nbsearch.cpp b/src/gromacs/selection/nbsearch.cpp
index d626b66d4e..7e32fa6536 100644
--- a/src/gromacs/selection/nbsearch.cpp
+++ b/src/gromacs/selection/nbsearch.cpp
@@ -54,7 +54,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/selection/nbsearch.h"
+#include "nbsearch.h"
 
 #include <cmath>
 #include <cstring>
@@ -65,7 +65,6 @@
 #include "thread_mpi/mutex.h"
 
 #include "gromacs/legacyheaders/names.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/selection/position.h"
diff --git a/src/gromacs/selection/nbsearch.h b/src/gromacs/selection/nbsearch.h
index be25e7a3fd..fd7b41b129 100644
--- a/src/gromacs/selection/nbsearch.h
+++ b/src/gromacs/selection/nbsearch.h
@@ -51,11 +51,11 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../math/vectypes.h"
-#include "../utility/arrayref.h"
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-#include "../utility/real.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
 
 struct t_blocka;
 struct t_pbc;
diff --git a/src/gromacs/selection/params.cpp b/src/gromacs/selection/params.cpp
index b8cac2501a..9c76fe7aea 100644
--- a/src/gromacs/selection/params.cpp
+++ b/src/gromacs/selection/params.cpp
@@ -46,8 +46,6 @@
 
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
-#include "gromacs/selection/selparam.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
@@ -56,9 +54,10 @@
 #include "gromacs/utility/stringutil.h"
 
 #include "parsetree.h"
-#include "position.h"
 #include "scanner.h"
 #include "selelem.h"
+#include "selmethod.h"
+#include "selparam.h"
 
 using gmx::SelectionParserValue;
 using gmx::SelectionParserValueList;
diff --git a/src/gromacs/selection/parser_internal.h b/src/gromacs/selection/parser_internal.h
index b74ce1a313..b938adfa6c 100644
--- a/src/gromacs/selection/parser_internal.h
+++ b/src/gromacs/selection/parser_internal.h
@@ -46,6 +46,8 @@
 #ifndef GMX_SELECTION_PARSER_INTERNAL_H
 #define GMX_SELECTION_PARSER_INTERNAL_H
 
+#include "config.h"
+
 #include <exception>
 
 #include <boost/scoped_ptr.hpp>
@@ -53,11 +55,8 @@
 #include "gromacs/utility/gmxassert.h"
 
 #include "parsetree.h"
-#include "selelem.h"
-
 #include "scanner.h"
-
-#include "config.h"
+#include "selelem.h"
 
 //! Error handler needed by Bison.
 static void
diff --git a/src/gromacs/selection/parsetree.cpp b/src/gromacs/selection/parsetree.cpp
index a978356c70..14d5d27dbd 100644
--- a/src/gromacs/selection/parsetree.cpp
+++ b/src/gromacs/selection/parsetree.cpp
@@ -221,15 +221,15 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
+#include "parsetree.h"
+
 #include <stdarg.h>
+#include <stdio.h>
 
 #include <boost/exception_ptr.hpp>
 #include <boost/shared_ptr.hpp>
 
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
@@ -238,13 +238,13 @@
 #include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"
-#include "parsetree.h"
+#include "poscalc.h"
+#include "scanner.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
+#include "selmethod.h"
 #include "symrec.h"
 
-#include "scanner.h"
-
 using gmx::SelectionParserValue;
 using gmx::SelectionParserValueList;
 using gmx::SelectionParserValueListPointer;
diff --git a/src/gromacs/selection/poscalc.cpp b/src/gromacs/selection/poscalc.cpp
index 822791a6a0..f193abd42c 100644
--- a/src/gromacs/selection/poscalc.cpp
+++ b/src/gromacs/selection/poscalc.cpp
@@ -61,20 +61,22 @@
  */
 #include "gmxpre.h"
 
+#include "poscalc.h"
+
 #include <string.h>
 
 #include <algorithm>
 
 #include "gromacs/fileio/trx.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/selection/centerofmass.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "centerofmass.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/selection/poscalc.h b/src/gromacs/selection/poscalc.h
index 47806069b1..83b95d6d32 100644
--- a/src/gromacs/selection/poscalc.h
+++ b/src/gromacs/selection/poscalc.h
@@ -54,7 +54,7 @@
 
 #include <cstdio>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 /*! \name Flags for position calculation.
  * \anchor poscalc_flags
diff --git a/src/gromacs/selection/position.cpp b/src/gromacs/selection/position.cpp
index e71a9aad98..e5c6346f94 100644
--- a/src/gromacs/selection/position.cpp
+++ b/src/gromacs/selection/position.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/selection/position.h"
+#include "position.h"
 
 #include <string.h>
 
diff --git a/src/gromacs/selection/position.h b/src/gromacs/selection/position.h
index cfe2e93189..e8e662d1ec 100644
--- a/src/gromacs/selection/position.h
+++ b/src/gromacs/selection/position.h
@@ -41,9 +41,8 @@
 #ifndef GMX_SELECTION_POSITION_H
 #define GMX_SELECTION_POSITION_H
 
-#include "../math/vectypes.h"
-
-#include "indexutil.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/selection/indexutil.h"
 
 /*! \brief
  * Stores a set of positions together with their origins.
diff --git a/src/gromacs/selection/scanner_internal.cpp b/src/gromacs/selection/scanner_internal.cpp
index d7feb7d042..f13031fd1a 100644
--- a/src/gromacs/selection/scanner_internal.cpp
+++ b/src/gromacs/selection/scanner_internal.cpp
@@ -53,6 +53,8 @@
  */
 #include "gmxpre.h"
 
+#include "scanner_internal.h"
+
 #include <stdlib.h>
 #include <string.h>
 
@@ -65,16 +67,14 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "parser.h"
 #include "parsetree.h"
+#include "scanner.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
 #include "selmethod.h"
 #include "symrec.h"
 
-#include "parser.h"
-#include "scanner.h"
-#include "scanner_internal.h"
-
 /*! \brief
  * Step in which the allocated memory for pretty-printed input is incremented.
  */
diff --git a/src/gromacs/selection/selection.cpp b/src/gromacs/selection/selection.cpp
index c114a4fa59..99bd2abd5c 100644
--- a/src/gromacs/selection/selection.cpp
+++ b/src/gromacs/selection/selection.cpp
@@ -43,10 +43,10 @@
 
 #include "selection.h"
 
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/position.h"
 #include "gromacs/topology/topology.h"
 
-#include "nbsearch.h"
-#include "position.h"
 #include "selelem.h"
 #include "selvalue.h"
 
diff --git a/src/gromacs/selection/selection.h b/src/gromacs/selection/selection.h
index 30f060c557..55772ffbf5 100644
--- a/src/gromacs/selection/selection.h
+++ b/src/gromacs/selection/selection.h
@@ -46,12 +46,11 @@
 #include <string>
 #include <vector>
 
-#include "../utility/arrayref.h"
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-
-#include "position.h"
-#include "selectionenums.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selectionenums.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/gmxassert.h"
 
 struct t_topology;
 
diff --git a/src/gromacs/selection/selectioncollection-impl.h b/src/gromacs/selection/selectioncollection-impl.h
index a478143880..abc9386830 100644
--- a/src/gromacs/selection/selectioncollection-impl.h
+++ b/src/gromacs/selection/selectioncollection-impl.h
@@ -50,12 +50,13 @@
 
 #include <boost/scoped_ptr.hpp>
 
-#include "../onlinehelp/helptopicinterface.h"
-#include "../utility/uniqueptr.h"
-#include "indexutil.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/utility/uniqueptr.h"
+
 #include "poscalc.h"
-#include "selection.h" // For gmx::SelectionList
-#include "selectioncollection.h"
 #include "selelem.h"
 
 struct gmx_sel_mempool_t;
diff --git a/src/gromacs/selection/selectioncollection.cpp b/src/gromacs/selection/selectioncollection.cpp
index 288bcea5e0..f4bfd210a0 100644
--- a/src/gromacs/selection/selectioncollection.cpp
+++ b/src/gromacs/selection/selectioncollection.cpp
@@ -51,14 +51,14 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "gromacs/legacyheaders/oenv.h"
-
 #include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/onlinehelp/helpmanager.h"
 #include "gromacs/onlinehelp/helpwritercontext.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/selection.h"
+#include "gromacs/selection/selhelp.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
@@ -72,10 +72,8 @@
 #include "parser.h"
 #include "poscalc.h"
 #include "scanner.h"
-#include "selection.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
-#include "selhelp.h"
 #include "selmethod.h"
 #include "symrec.h"
 
diff --git a/src/gromacs/selection/selectioncollection.h b/src/gromacs/selection/selectioncollection.h
index 87f923c7bc..281b473abc 100644
--- a/src/gromacs/selection/selectioncollection.h
+++ b/src/gromacs/selection/selectioncollection.h
@@ -48,10 +48,9 @@
 #include <string>
 #include <vector>
 
-#include "../legacyheaders/types/oenv.h"
-
-#include "../utility/common.h"
-#include "selection.h" // For gmx::SelectionList
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
 
 struct gmx_ana_indexgrps_t;
 struct t_pbc;
diff --git a/src/gromacs/selection/selectionenums.h b/src/gromacs/selection/selectionenums.h
index d401ac56c1..2523ea8876 100644
--- a/src/gromacs/selection/selectionenums.h
+++ b/src/gromacs/selection/selectionenums.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_SELECTION_SELECTIONENUMS_H
 #define GMX_SELECTION_SELECTIONENUMS_H
 
-#include "../utility/flags.h"
+#include "gromacs/utility/flags.h"
 
 /*! \brief
  * Defines the type of covered fraction.
diff --git a/src/gromacs/selection/selectionfileoption.h b/src/gromacs/selection/selectionfileoption.h
index 324d33fdc7..369d6256db 100644
--- a/src/gromacs/selection/selectionfileoption.h
+++ b/src/gromacs/selection/selectionfileoption.h
@@ -43,7 +43,7 @@
 #ifndef GMX_SELECTION_SELECTIONFILEOPTION_H
 #define GMX_SELECTION_SELECTIONFILEOPTION_H
 
-#include "../options/abstractoption.h"
+#include "gromacs/options/abstractoption.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/selection/selectionfileoptionstorage.h b/src/gromacs/selection/selectionfileoptionstorage.h
index ac628bf7ba..9d87794598 100644
--- a/src/gromacs/selection/selectionfileoptionstorage.h
+++ b/src/gromacs/selection/selectionfileoptionstorage.h
@@ -42,8 +42,8 @@
 #ifndef GMX_SELECTION_SELECTIONFILEOPTIONSTORAGE_H
 #define GMX_SELECTION_SELECTIONFILEOPTIONSTORAGE_H
 
-#include "../options/abstractoptionstorage.h"
-#include "selectionfileoption.h"
+#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/selection/selectionfileoption.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/selection/selectionoption.cpp b/src/gromacs/selection/selectionoption.cpp
index 923384d7e7..f278723cc1 100644
--- a/src/gromacs/selection/selectionoption.cpp
+++ b/src/gromacs/selection/selectionoption.cpp
@@ -42,19 +42,20 @@
 #include "gmxpre.h"
 
 #include "selectionoption.h"
-#include "selectionfileoption.h"
-#include "selectionoptionstorage.h"
-#include "selectionfileoptionstorage.h"
 
 #include <string>
 
 #include "gromacs/options/optionmanagercontainer.h"
 #include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionfileoption.h"
 #include "gromacs/selection/selectionoptionmanager.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/messagestringcollector.h"
 
+#include "selectionfileoptionstorage.h"
+#include "selectionoptionstorage.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/selection/selectionoption.h b/src/gromacs/selection/selectionoption.h
index 4655585f37..0af37dddc7 100644
--- a/src/gromacs/selection/selectionoption.h
+++ b/src/gromacs/selection/selectionoption.h
@@ -43,10 +43,9 @@
 #ifndef GMX_SELECTION_SELECTIONOPTION_H
 #define GMX_SELECTION_SELECTIONOPTION_H
 
-#include "../options/abstractoption.h"
-
-#include "selection.h"
-#include "selectionenums.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionenums.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/selection/selectionoptionmanager.cpp b/src/gromacs/selection/selectionoptionmanager.cpp
index a545c67363..ee1e486d0c 100644
--- a/src/gromacs/selection/selectionoptionmanager.cpp
+++ b/src/gromacs/selection/selectionoptionmanager.cpp
@@ -47,8 +47,8 @@
 
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectioncollection.h"
-#include "gromacs/selection/selectionoption.h"
 #include "gromacs/selection/selectionfileoption.h"
+#include "gromacs/selection/selectionoption.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"
 
diff --git a/src/gromacs/selection/selectionoptionmanager.h b/src/gromacs/selection/selectionoptionmanager.h
index ec26193b58..66a075dcaf 100644
--- a/src/gromacs/selection/selectionoptionmanager.h
+++ b/src/gromacs/selection/selectionoptionmanager.h
@@ -45,8 +45,8 @@
 
 #include <string>
 
-#include "../options/options.h"
-#include "../utility/common.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/selection/selectionoptionstorage.h b/src/gromacs/selection/selectionoptionstorage.h
index fb9300d2b1..41ef1488db 100644
--- a/src/gromacs/selection/selectionoptionstorage.h
+++ b/src/gromacs/selection/selectionoptionstorage.h
@@ -44,10 +44,10 @@
 
 #include <string>
 
-#include "../options/optionstoragetemplate.h"
-#include "selection.h"
-#include "selectionenums.h"
-#include "selectionoption.h"
+#include "gromacs/options/optionstoragetemplate.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionenums.h"
+#include "gromacs/selection/selectionoption.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/selection/selelem.cpp b/src/gromacs/selection/selelem.cpp
index 367737e338..76f65be971 100644
--- a/src/gromacs/selection/selelem.cpp
+++ b/src/gromacs/selection/selelem.cpp
@@ -41,12 +41,12 @@
  */
 #include "gmxpre.h"
 
+#include "selelem.h"
+
 #include <cstring>
 
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
@@ -54,7 +54,7 @@
 
 #include "keywords.h"
 #include "mempool.h"
-#include "selelem.h"
+#include "poscalc.h"
 #include "selmethod.h"
 
 /*!
diff --git a/src/gromacs/selection/selelem.h b/src/gromacs/selection/selelem.h
index 1a1e86bf61..ddc429850f 100644
--- a/src/gromacs/selection/selelem.h
+++ b/src/gromacs/selection/selelem.h
@@ -53,10 +53,10 @@
 
 #include <boost/shared_ptr.hpp>
 
+#include "gromacs/selection/indexutil.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/real.h"
 
-#include "indexutil.h"
 #include "selvalue.h"
 
 struct gmx_ana_poscalc_t;
diff --git a/src/gromacs/selection/selhelp.cpp b/src/gromacs/selection/selhelp.cpp
index 0b707c8b27..4a52815f37 100644
--- a/src/gromacs/selection/selhelp.cpp
+++ b/src/gromacs/selection/selhelp.cpp
@@ -41,9 +41,11 @@
  */
 #include "gmxpre.h"
 
+#include "selhelp.h"
+
 #include <string>
-#include <vector>
 #include <utility>
+#include <vector>
 
 #include <boost/scoped_ptr.hpp>
 
@@ -53,7 +55,6 @@
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "selhelp.h"
 #include "selmethod.h"
 #include "symrec.h"
 
diff --git a/src/gromacs/selection/selhelp.h b/src/gromacs/selection/selhelp.h
index 225434b3f9..b29251d31a 100644
--- a/src/gromacs/selection/selhelp.h
+++ b/src/gromacs/selection/selhelp.h
@@ -43,7 +43,7 @@
 #ifndef GMX_SELECTION_SELHELP_H
 #define GMX_SELECTION_SELHELP_H
 
-#include "../onlinehelp/helptopicinterface.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/selection/selmethod.cpp b/src/gromacs/selection/selmethod.cpp
index b8a8645a9b..6524f2fec9 100644
--- a/src/gromacs/selection/selmethod.cpp
+++ b/src/gromacs/selection/selmethod.cpp
@@ -41,12 +41,12 @@
  */
 #include "gmxpre.h"
 
+#include "selmethod.h"
+
 #include <ctype.h>
 #include <stdarg.h>
 
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 
diff --git a/src/gromacs/selection/selparam.h b/src/gromacs/selection/selparam.h
index 9f471ccf5e..bedfaadff1 100644
--- a/src/gromacs/selection/selparam.h
+++ b/src/gromacs/selection/selparam.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -48,7 +48,8 @@
 #ifndef GMX_SELECTION_SELPARAM_H
 #define GMX_SELECTION_SELPARAM_H
 
-#include "indexutil.h"
+#include "gromacs/selection/indexutil.h"
+
 #include "selvalue.h"
 
 /*! \name Parameter flags
diff --git a/src/gromacs/selection/selvalue.cpp b/src/gromacs/selection/selvalue.cpp
index c41ba668a9..86edfba070 100644
--- a/src/gromacs/selection/selvalue.cpp
+++ b/src/gromacs/selection/selvalue.cpp
@@ -41,9 +41,10 @@
  */
 #include "gmxpre.h"
 
+#include "selvalue.h"
+
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selvalue.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/selection/selvalue.h b/src/gromacs/selection/selvalue.h
index 759fdfc046..63f260b2b4 100644
--- a/src/gromacs/selection/selvalue.h
+++ b/src/gromacs/selection/selvalue.h
@@ -45,7 +45,7 @@
 #ifndef GMX_SELECTION_SELVALUE_H
 #define GMX_SELECTION_SELVALUE_H
 
-#include "../utility/real.h"
+#include "gromacs/utility/real.h"
 
 /** Defines the value type of a different selection objects. */
 typedef enum
diff --git a/src/gromacs/selection/sm_compare.cpp b/src/gromacs/selection/sm_compare.cpp
index 5ff24d7423..51aa8a6d47 100644
--- a/src/gromacs/selection/sm_compare.cpp
+++ b/src/gromacs/selection/sm_compare.cpp
@@ -44,13 +44,13 @@
 #include <cmath>
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/utilities.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "selmethod.h"
+
 /** Defines the comparison operator for comparison expressions. */
 typedef enum
 {
diff --git a/src/gromacs/selection/sm_distance.cpp b/src/gromacs/selection/sm_distance.cpp
index a7725533f3..636d28c112 100644
--- a/src/gromacs/selection/sm_distance.cpp
+++ b/src/gromacs/selection/sm_distance.cpp
@@ -45,13 +45,13 @@
 #include "gmxpre.h"
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/nbsearch.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 
+#include "selmethod.h"
+
 /*! \internal
  * \brief
  * Data structure for distance-based selection method.
diff --git a/src/gromacs/selection/sm_insolidangle.cpp b/src/gromacs/selection/sm_insolidangle.cpp
index 1c37cb4b32..9c163e097f 100644
--- a/src/gromacs/selection/sm_insolidangle.cpp
+++ b/src/gromacs/selection/sm_insolidangle.cpp
@@ -114,12 +114,11 @@
  */
 #include "gmxpre.h"
 
-#include <algorithm>
-
 #include <math.h>
 
-#include "gromacs/legacyheaders/macros.h"
+#include <algorithm>
 
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
@@ -127,11 +126,11 @@
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "selelem.h"
+#include "selmethod.h"
 
 using std::min;
 using std::max;
diff --git a/src/gromacs/selection/sm_keywords.cpp b/src/gromacs/selection/sm_keywords.cpp
index 13d126ca45..32d478ed00 100644
--- a/src/gromacs/selection/sm_keywords.cpp
+++ b/src/gromacs/selection/sm_keywords.cpp
@@ -50,19 +50,18 @@
 #include <boost/shared_ptr.hpp>
 
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxregex.h"
 #include "gromacs/utility/messagestringcollector.h"
-#include "gromacs/utility/stringutil.h"
 #include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"
 #include "parsetree.h"
 #include "scanner.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 /*! \brief
  * Allocates data for integer keyword evaluation.
diff --git a/src/gromacs/selection/sm_merge.cpp b/src/gromacs/selection/sm_merge.cpp
index 828bea37d4..9c8d2e3041 100644
--- a/src/gromacs/selection/sm_merge.cpp
+++ b/src/gromacs/selection/sm_merge.cpp
@@ -42,14 +42,14 @@
 #include "gmxpre.h"
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "selmethod.h"
+
 /*! \internal \brief
  * Data structure for the merging selection modifiers.
  */
diff --git a/src/gromacs/selection/sm_permute.cpp b/src/gromacs/selection/sm_permute.cpp
index ebd7c72b5a..a4f52fe150 100644
--- a/src/gromacs/selection/sm_permute.cpp
+++ b/src/gromacs/selection/sm_permute.cpp
@@ -42,14 +42,14 @@
 #include "gmxpre.h"
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "selmethod.h"
+
 /*! \internal \brief
  * Data structure for the \p permute selection modifier.
  */
diff --git a/src/gromacs/selection/sm_position.cpp b/src/gromacs/selection/sm_position.cpp
index b010881846..3a92f82d69 100644
--- a/src/gromacs/selection/sm_position.cpp
+++ b/src/gromacs/selection/sm_position.cpp
@@ -42,16 +42,15 @@
 #include "gmxpre.h"
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "keywords.h"
+#include "poscalc.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 /*! \internal \brief
  * Data structure for position keyword evaluation.
diff --git a/src/gromacs/selection/sm_same.cpp b/src/gromacs/selection/sm_same.cpp
index 5009ede957..cb8126171b 100644
--- a/src/gromacs/selection/sm_same.cpp
+++ b/src/gromacs/selection/sm_same.cpp
@@ -44,14 +44,13 @@
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "keywords.h"
 #include "parsetree.h"
 #include "selelem.h"
+#include "selmethod.h"
 
 /*! \internal
  * \brief
diff --git a/src/gromacs/selection/sm_simple.cpp b/src/gromacs/selection/sm_simple.cpp
index 709aa247b7..de1a6fc650 100644
--- a/src/gromacs/selection/sm_simple.cpp
+++ b/src/gromacs/selection/sm_simple.cpp
@@ -44,12 +44,12 @@
 #include <cctype>
 
 #include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/topology/topology.h"
 #include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/topology/topology.h"
 #include "gromacs/utility/exceptions.h"
 
+#include "selmethod.h"
+
 /** Evaluates the \p all selection keyword. */
 static void
 evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,
diff --git a/src/gromacs/selection/symrec.cpp b/src/gromacs/selection/symrec.cpp
index 3df67883db..cd648f60ef 100644
--- a/src/gromacs/selection/symrec.cpp
+++ b/src/gromacs/selection/symrec.cpp
@@ -41,12 +41,13 @@
  */
 #include "gmxpre.h"
 
+#include "symrec.h"
+
 #include <map>
 #include <string>
 #include <utility>
 
 #include "gromacs/legacyheaders/macros.h"
-
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
@@ -54,7 +55,6 @@
 
 #include "poscalc.h"
 #include "selelem.h"
-#include "symrec.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/selection/tests/indexutil.cpp b/src/gromacs/selection/tests/indexutil.cpp
index caf5d0462d..5efd13423e 100644
--- a/src/gromacs/selection/tests/indexutil.cpp
+++ b/src/gromacs/selection/tests/indexutil.cpp
@@ -44,9 +44,10 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/selection/indexutil.h"
+
 #include <gtest/gtest.h>
 
-#include "gromacs/selection/indexutil.h"
 #include "gromacs/topology/block.h"
 
 #include "testutils/refdata.h"
diff --git a/src/gromacs/selection/tests/nbsearch.cpp b/src/gromacs/selection/tests/nbsearch.cpp
index ac7cba62a5..c3bc49f92b 100644
--- a/src/gromacs/selection/tests/nbsearch.cpp
+++ b/src/gromacs/selection/tests/nbsearch.cpp
@@ -48,8 +48,6 @@
 
 #include "gromacs/selection/nbsearch.h"
 
-#include <gtest/gtest.h>
-
 #include <cmath>
 
 #include <algorithm>
@@ -57,6 +55,8 @@
 #include <numeric>
 #include <vector>
 
+#include <gtest/gtest.h>
+
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
diff --git a/src/gromacs/selection/tests/poscalc.cpp b/src/gromacs/selection/tests/poscalc.cpp
index 4ca53be929..1608a5b11b 100644
--- a/src/gromacs/selection/tests/poscalc.cpp
+++ b/src/gromacs/selection/tests/poscalc.cpp
@@ -41,14 +41,15 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
+#include "gromacs/selection/poscalc.h"
 
 #include <vector>
 
+#include <gtest/gtest.h>
+
 #include "gromacs/fileio/trx.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/selection/tests/selectioncollection.cpp b/src/gromacs/selection/tests/selectioncollection.cpp
index 4e252346f9..9e6fd86281 100644
--- a/src/gromacs/selection/tests/selectioncollection.cpp
+++ b/src/gromacs/selection/tests/selectioncollection.cpp
@@ -41,13 +41,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/selection/selectioncollection.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/fileio/trx.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/selectioncollection.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arrayref.h"
diff --git a/src/gromacs/selection/tests/selectionoption.cpp b/src/gromacs/selection/tests/selectionoption.cpp
index 072170fccf..8f3397cf43 100644
--- a/src/gromacs/selection/tests/selectionoption.cpp
+++ b/src/gromacs/selection/tests/selectionoption.cpp
@@ -41,6 +41,8 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/selection/selectionoption.h"
+
 #include <gtest/gtest.h>
 
 #include "gromacs/options/options.h"
@@ -48,7 +50,6 @@
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectioncollection.h"
 #include "gromacs/selection/selectionfileoption.h"
-#include "gromacs/selection/selectionoption.h"
 #include "gromacs/selection/selectionoptionmanager.h"
 #include "gromacs/utility/exceptions.h"
 
diff --git a/src/gromacs/selection/tests/toputils.cpp b/src/gromacs/selection/tests/toputils.cpp
index b27c636f09..eff1e0c356 100644
--- a/src/gromacs/selection/tests/toputils.cpp
+++ b/src/gromacs/selection/tests/toputils.cpp
@@ -45,10 +45,10 @@
 
 #include <cstring>
 
-#include "gromacs/math/vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/gmxassert.h"
diff --git a/src/gromacs/simd/impl_intel_mic/impl_intel_mic.h b/src/gromacs/simd/impl_intel_mic/impl_intel_mic.h
index 8508941b56..67418f98d0 100644
--- a/src/gromacs/simd/impl_intel_mic/impl_intel_mic.h
+++ b/src/gromacs/simd/impl_intel_mic/impl_intel_mic.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_INTEL_MIC_H
 #define GMX_SIMD_IMPL_INTEL_MIC_H
 
+#include "config.h"
+
 #include <math.h>
-#include <immintrin.h>
 
-#include "config.h"
+#include <immintrin.h>
 
 /* Intel Xeon Phi, or
  * the-artist-formerly-known-as-Knight's-corner, or
diff --git a/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h b/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h
index 195fdbc295..e19320add3 100644
--- a/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h
+++ b/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_X86_AVX2_256_H
 #define GMX_SIMD_IMPL_X86_AVX2_256_H
 
+#include "config.h"
+
 #include <math.h>
-#include <immintrin.h>
 
-#include "config.h"
+#include <immintrin.h>
 
 /* x86 256-bit AVX2 SIMD instruction wrappers
  *
diff --git a/src/gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h b/src/gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h
index 7c946d10d2..c13e847ffa 100644
--- a/src/gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h
+++ b/src/gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h
@@ -36,12 +36,13 @@
 #ifndef GMX_SIMD_IMPL_X86_AVX_128_FMA_H
 #define GMX_SIMD_IMPL_X86_AVX_128_FMA_H
 
+#include "config.h"
+
 #include <math.h>
+
 #include <immintrin.h>
 #include <x86intrin.h>
 
-#include "config.h"
-
 /* x86 128-bit AVX with FMA SIMD instruction wrappers
  *
  * Please see documentation in gromacs/simd/simd.h for details
diff --git a/src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h b/src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h
index e688d14c94..999b417d68 100644
--- a/src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h
+++ b/src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_X86_AVX_256_H
 #define GMX_SIMD_IMPL_X86_AVX_256_H
 
+#include "config.h"
+
 #include <math.h>
-#include <immintrin.h>
 
-#include "config.h"
+#include <immintrin.h>
 
 /* It is cleaner to start the AVX implementation from scratch rather than
  * first inheriting from SSE4.1, which in turn inherits from SSE2. However,
diff --git a/src/gromacs/simd/impl_x86_sse2/impl_x86_sse2.h b/src/gromacs/simd/impl_x86_sse2/impl_x86_sse2.h
index c16d3d4d57..2d3f908f56 100644
--- a/src/gromacs/simd/impl_x86_sse2/impl_x86_sse2.h
+++ b/src/gromacs/simd/impl_x86_sse2/impl_x86_sse2.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_X86_SSE2_H
 #define GMX_SIMD_IMPL_X86_SSE2_H
 
+#include "config.h"
+
 #include <math.h>
-#include <emmintrin.h>
 
-#include "config.h"
+#include <emmintrin.h>
 
 /* Set capabilities that can be inherited */
 #define GMX_SIMD_X86_SSE2_OR_HIGHER
diff --git a/src/gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h b/src/gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h
index 91bef05ac6..8b8384a835 100644
--- a/src/gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h
+++ b/src/gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h
@@ -36,10 +36,11 @@
 #ifndef GMX_SIMD_IMPL_X86_SSE4_1_H
 #define GMX_SIMD_IMPL_X86_SSE4_1_H
 
+#include "config.h"
+
 #include <math.h>
-#include <smmintrin.h>
 
-#include "config.h"
+#include <smmintrin.h>
 
 /* x86 SSE4.1 SIMD instruction wrappers
  *
diff --git a/src/gromacs/simd/math_x86_avx_128_fma_double.h b/src/gromacs/simd/math_x86_avx_128_fma_double.h
index fed6d54694..9ee80edbd7 100644
--- a/src/gromacs/simd/math_x86_avx_128_fma_double.h
+++ b/src/gromacs/simd/math_x86_avx_128_fma_double.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_AVX_128_FMA_DOUBLE_H
 #define GMX_SIMD_MATH_AVX_128_FMA_DOUBLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need
diff --git a/src/gromacs/simd/math_x86_avx_128_fma_single.h b/src/gromacs/simd/math_x86_avx_128_fma_single.h
index fc7113dd3a..014508d977 100644
--- a/src/gromacs/simd/math_x86_avx_128_fma_single.h
+++ b/src/gromacs/simd/math_x86_avx_128_fma_single.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_AVX_128_FMA_SINGLE_H
 #define GMX_SIMD_MATH_AVX_128_FMA_SINGLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need
diff --git a/src/gromacs/simd/math_x86_avx_256_double.h b/src/gromacs/simd/math_x86_avx_256_double.h
index 8eb7941765..6a1963cbaf 100644
--- a/src/gromacs/simd/math_x86_avx_256_double.h
+++ b/src/gromacs/simd/math_x86_avx_256_double.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_AVX_256_DOUBLE_H
 #define GMX_SIMD_MATH_AVX_256_DOUBLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need
diff --git a/src/gromacs/simd/math_x86_avx_256_single.h b/src/gromacs/simd/math_x86_avx_256_single.h
index b23712a259..ad72a10579 100644
--- a/src/gromacs/simd/math_x86_avx_256_single.h
+++ b/src/gromacs/simd/math_x86_avx_256_single.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_AVX_256_SINGLE_H
 #define GMX_SIMD_MATH_AVX_256_SINGLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need
diff --git a/src/gromacs/simd/math_x86_sse2_double.h b/src/gromacs/simd/math_x86_sse2_double.h
index 9332dc3d36..857f4ee2ef 100644
--- a/src/gromacs/simd/math_x86_sse2_double.h
+++ b/src/gromacs/simd/math_x86_sse2_double.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_SSE2_DOUBLE_H
 #define GMX_SIMD_MATH_SSE2_DOUBLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need
diff --git a/src/gromacs/simd/math_x86_sse2_single.h b/src/gromacs/simd/math_x86_sse2_single.h
index 054fd2c1bc..67ebf7f7cd 100644
--- a/src/gromacs/simd/math_x86_sse2_single.h
+++ b/src/gromacs/simd/math_x86_sse2_single.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_SSE2_SINGLE_H
 #define GMX_SIMD_MATH_SSE2_SINGLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need
diff --git a/src/gromacs/simd/math_x86_sse4_1_double.h b/src/gromacs/simd/math_x86_sse4_1_double.h
index 4d8955a51c..e7f7a06249 100644
--- a/src/gromacs/simd/math_x86_sse4_1_double.h
+++ b/src/gromacs/simd/math_x86_sse4_1_double.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_SSE4_1_DOUBLE_H
 #define GMX_SIMD_MATH_SSE4_1_DOUBLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need
diff --git a/src/gromacs/simd/math_x86_sse4_1_single.h b/src/gromacs/simd/math_x86_sse4_1_single.h
index 2fbdf23b3a..7c78dd57b9 100644
--- a/src/gromacs/simd/math_x86_sse4_1_single.h
+++ b/src/gromacs/simd/math_x86_sse4_1_single.h
@@ -35,7 +35,7 @@
 #ifndef GMX_SIMD_MATH_SSE4_1_SINGLE_H
 #define GMX_SIMD_MATH_SSE4_1_SINGLE_H
 
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
 
 /* Temporary:
  * Alias some old SSE definitions to new SIMD definitions so we don't need
diff --git a/src/gromacs/simd/simd.h b/src/gromacs/simd/simd.h
index a979fd3e45..988ae65044 100644
--- a/src/gromacs/simd/simd.h
+++ b/src/gromacs/simd/simd.h
@@ -112,32 +112,32 @@ static gmx_inline double * gmx_simd4_align_d(double *p);
  * file with different SIMD definitions for different files.
  */
 #if defined __MIC__
-#    include "gromacs/simd/impl_intel_mic/impl_intel_mic.h"
+#    include "impl_intel_mic/impl_intel_mic.h"
 #elif defined GMX_SIMD_X86_AVX2_256
-#    include "gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h"
+#    include "impl_x86_avx2_256/impl_x86_avx2_256.h"
 #elif defined GMX_SIMD_X86_AVX_256
-#    include "gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h"
+#    include "impl_x86_avx_256/impl_x86_avx_256.h"
 #elif defined GMX_SIMD_X86_AVX_128_FMA
-#    include "gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h"
+#    include "impl_x86_avx_128_fma/impl_x86_avx_128_fma.h"
 #elif defined GMX_SIMD_X86_SSE4_1
-#    include "gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h"
+#    include "impl_x86_sse4_1/impl_x86_sse4_1.h"
 #elif defined GMX_SIMD_X86_SSE2
-#    include "gromacs/simd/impl_x86_sse2/impl_x86_sse2.h"
+#    include "impl_x86_sse2/impl_x86_sse2.h"
 #elif defined GMX_SIMD_ARM_NEON
-#    include "gromacs/simd/impl_arm_neon/impl_arm_neon.h"
+#    include "impl_arm_neon/impl_arm_neon.h"
 #elif defined GMX_SIMD_ARM_NEON_ASIMD
-#    include "gromacs/simd/impl_arm_neon_asimd/impl_arm_neon_asimd.h"
+#    include "impl_arm_neon_asimd/impl_arm_neon_asimd.h"
 #elif defined GMX_SIMD_IBM_QPX
-#    include "gromacs/simd/impl_ibm_qpx/impl_ibm_qpx.h"
+#    include "impl_ibm_qpx/impl_ibm_qpx.h"
 #elif defined GMX_SIMD_SPARC64_HPC_ACE
-#    include "gromacs/simd/impl_sparc64_hpc_ace/impl_sparc64_hpc_ace.h"
+#    include "impl_sparc64_hpc_ace/impl_sparc64_hpc_ace.h"
 #elif (defined GMX_SIMD_REFERENCE) || (defined DOXYGEN)
 /* Plain C SIMD reference implementation, also serves as documentation.
  * For now this code path will also be taken for Sparc64_HPC_ACE since we have
  * not yet added the verlet kernel extensions there. The group kernels do not
  * depend on this file, so they will still be accelerated with SIMD.
  */
-#    include "gromacs/simd/impl_reference/impl_reference.h"
+#    include "impl_reference/impl_reference.h"
 #else
 /* Turn off the GMX_SIMD flag if we do not even have reference support */
 #    undef GMX_SIMD
diff --git a/src/gromacs/simd/simd_math.h b/src/gromacs/simd/simd_math.h
index 177aed4b07..85d545c3d0 100644
--- a/src/gromacs/simd/simd_math.h
+++ b/src/gromacs/simd/simd_math.h
@@ -55,13 +55,13 @@
  * \ingroup module_simd
  */
 
+#include "config.h"
+
 #include <math.h>
 
 #include "gromacs/math/utilities.h"
 #include "gromacs/simd/simd.h"
 
-#include "config.h"
-
 /*! \cond libapi */
 /*! \addtogroup module_simd */
 /*! \{ */
diff --git a/src/gromacs/simd/tests/base.cpp b/src/gromacs/simd/tests/base.cpp
index fed7848045..115707363a 100644
--- a/src/gromacs/simd/tests/base.cpp
+++ b/src/gromacs/simd/tests/base.cpp
@@ -34,13 +34,14 @@
  */
 #include "gmxpre.h"
 
+#include "base.h"
+
 #include <math.h>
 
-#include "testutils/testoptions.h"
-#include "gromacs/options/options.h"
 #include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
 
-#include "base.h"
+#include "testutils/testoptions.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/simd/tests/simd.h b/src/gromacs/simd/tests/simd.h
index 551546fbf6..26cdf9e74b 100644
--- a/src/gromacs/simd/tests/simd.h
+++ b/src/gromacs/simd/tests/simd.h
@@ -75,7 +75,9 @@
  * \ingroup module_simd
  */
 #include <vector>
+
 #include <gtest/gtest.h>
+
 #include "gromacs/simd/simd.h"
 
 #include "base.h"
diff --git a/src/gromacs/simd/tests/simd4.h b/src/gromacs/simd/tests/simd4.h
index 3f3df63154..83cb794a74 100644
--- a/src/gromacs/simd/tests/simd4.h
+++ b/src/gromacs/simd/tests/simd4.h
@@ -48,9 +48,12 @@
  */
 
 #include <vector>
+
 #include <gtest/gtest.h>
+
 #include "gromacs/simd/simd.h"
-#include "gromacs/simd/tests/base.h"
+
+#include "base.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/simd/tests/simd4_floatingpoint.cpp b/src/gromacs/simd/tests/simd4_floatingpoint.cpp
index c51c71532f..68a448e3db 100644
--- a/src/gromacs/simd/tests/simd4_floatingpoint.cpp
+++ b/src/gromacs/simd/tests/simd4_floatingpoint.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include <math.h>
+
 #include "gromacs/math/utilities.h"
 
 #include "simd4.h"
diff --git a/src/gromacs/simd/tests/simd4_math.cpp b/src/gromacs/simd/tests/simd4_math.cpp
index 3e6555c967..2345c037e4 100644
--- a/src/gromacs/simd/tests/simd4_math.cpp
+++ b/src/gromacs/simd/tests/simd4_math.cpp
@@ -37,10 +37,11 @@
 #include "config.h"
 
 #include <vector>
+
 #include "gromacs/math/utilities.h"
+#include "gromacs/options/basicoptions.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
-#include "gromacs/options/basicoptions.h"
 
 #include "simd4.h"
 
diff --git a/src/gromacs/simd/tests/simd4_vector_operations.cpp b/src/gromacs/simd/tests/simd4_vector_operations.cpp
index 17a070b25e..02a29afd3d 100644
--- a/src/gromacs/simd/tests/simd4_vector_operations.cpp
+++ b/src/gromacs/simd/tests/simd4_vector_operations.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include <math.h>
+
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/vector_operations.h"
 
diff --git a/src/gromacs/simd/tests/simd_floatingpoint.cpp b/src/gromacs/simd/tests/simd_floatingpoint.cpp
index f0d07034a3..fb0a341482 100644
--- a/src/gromacs/simd/tests/simd_floatingpoint.cpp
+++ b/src/gromacs/simd/tests/simd_floatingpoint.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include <math.h>
+
 #include "gromacs/math/utilities.h"
 
 #include "simd.h"
diff --git a/src/gromacs/simd/tests/simd_math.cpp b/src/gromacs/simd/tests/simd_math.cpp
index 6899a9ee00..17c61ce05e 100644
--- a/src/gromacs/simd/tests/simd_math.cpp
+++ b/src/gromacs/simd/tests/simd_math.cpp
@@ -34,13 +34,15 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/simd/simd_math.h"
+
 #include "config.h"
 
 #include <vector>
+
 #include "gromacs/math/utilities.h"
-#include "gromacs/simd/simd.h"
-#include "gromacs/simd/simd_math.h"
 #include "gromacs/options/basicoptions.h"
+#include "gromacs/simd/simd.h"
 
 #include "simd.h"
 
diff --git a/src/gromacs/simd/tests/simd_vector_operations.cpp b/src/gromacs/simd/tests/simd_vector_operations.cpp
index 58c1e6f2af..9393c24c98 100644
--- a/src/gromacs/simd/tests/simd_vector_operations.cpp
+++ b/src/gromacs/simd/tests/simd_vector_operations.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include <math.h>
+
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/vector_operations.h"
 
diff --git a/src/gromacs/simd/vector_operations.h b/src/gromacs/simd/vector_operations.h
index d24c25f4db..30713524c7 100644
--- a/src/gromacs/simd/vector_operations.h
+++ b/src/gromacs/simd/vector_operations.h
@@ -46,10 +46,10 @@
 #ifndef GMX_SIMD_VECTOR_OPERATIONS_H
 #define GMX_SIMD_VECTOR_OPERATIONS_H
 
-#include "gromacs/simd/simd.h"
-
 #include "config.h"
 
+#include "gromacs/simd/simd.h"
+
 /*! \cond libapi */
 /*! \addtogroup module_simd */
 /*! \{ */
diff --git a/src/gromacs/statistics/statistics_test.c b/src/gromacs/statistics/statistics_test.c
index 7baff7bfac..4b3dbf8a66 100644
--- a/src/gromacs/statistics/statistics_test.c
+++ b/src/gromacs/statistics/statistics_test.c
@@ -36,12 +36,11 @@
  */
 #include "gmxpre.h"
 
-#include "statistics.h"
-
 #include <stdio.h>
 
 #include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
+#include "gromacs/statistics/statistics.h"
 #include "gromacs/utility/real.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/swap/swapcoords.c b/src/gromacs/swap/swapcoords.c
index 734b13b5e7..c81f4bba1e 100644
--- a/src/gromacs/swap/swapcoords.c
+++ b/src/gromacs/swap/swapcoords.c
@@ -41,28 +41,28 @@
  */
 #include "gmxpre.h"
 
+#include "swapcoords.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/timing/wallcycle.h"
-#include "swapcoords.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
 
 static char *SwS      = {"SWAP:"};                                           /**< For output that comes from the swap module */
 static char *SwSEmpty = {"     "};                                           /**< Placeholder for multi-line output */
diff --git a/src/gromacs/timing/cyclecounter.c b/src/gromacs/timing/cyclecounter.c
index a48bf35aa1..780587e114 100644
--- a/src/gromacs/timing/cyclecounter.c
+++ b/src/gromacs/timing/cyclecounter.c
@@ -37,10 +37,10 @@
 
 #include "cyclecounter.h"
 
-#include <time.h>
-
 #include "config.h"
 
+#include <time.h>
+
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
diff --git a/src/gromacs/timing/cyclecounter.h b/src/gromacs/timing/cyclecounter.h
index fcacc5e204..4b3bede736 100644
--- a/src/gromacs/timing/cyclecounter.h
+++ b/src/gromacs/timing/cyclecounter.h
@@ -148,8 +148,8 @@ typedef hrtime_t
 
 #elif defined(__xlC__) && defined (_AIX)
 /* AIX compilers */
-#include <sys/time.h>
 #include <sys/systemcfg.h>
+#include <sys/time.h>
 typedef unsigned long long
     gmx_cycles_t;
 
diff --git a/src/gromacs/timing/wallcycle.c b/src/gromacs/timing/wallcycle.c
index cedfaa6c83..c6f468e3ed 100644
--- a/src/gromacs/timing/wallcycle.c
+++ b/src/gromacs/timing/wallcycle.c
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/timing/wallcycle.h"
+#include "wallcycle.h"
 
 #include "config.h"
 
@@ -45,13 +45,12 @@
 
 #include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/timing/cyclecounter.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "cyclecounter.h"
-
 /* DEBUG_WCYCLE adds consistency checking for the counters.
  * It checks if you stop a counter different from the last
  * one that was opened and if you do nest too deep.
diff --git a/src/gromacs/timing/wallcycle.h b/src/gromacs/timing/wallcycle.h
index 70b0341081..a03a0ade68 100644
--- a/src/gromacs/timing/wallcycle.h
+++ b/src/gromacs/timing/wallcycle.h
@@ -39,9 +39,9 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/commrec_fwd.h"
-#include "../legacyheaders/types/nbnxn_cuda_types_ext.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/timing/walltime_accounting.c b/src/gromacs/timing/walltime_accounting.c
index d7c711127f..25c723d4d6 100644
--- a/src/gromacs/timing/walltime_accounting.c
+++ b/src/gromacs/timing/walltime_accounting.c
@@ -37,10 +37,10 @@
 
 #include "walltime_accounting.h"
 
-#include <time.h>
-
 #include "config.h"
 
+#include <time.h>
+
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
diff --git a/src/gromacs/timing/walltime_accounting.h b/src/gromacs/timing/walltime_accounting.h
index b80d138d8f..f131f26dd2 100644
--- a/src/gromacs/timing/walltime_accounting.h
+++ b/src/gromacs/timing/walltime_accounting.h
@@ -38,7 +38,7 @@
 #ifndef GMX_TIMING_WALLTIME_ACCOUNTING_H
 #define GMX_TIMING_WALLTIME_ACCOUNTING_H
 
-#include "../utility/basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.c
index 63fd7cffb1..ddb578dc06 100644
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.c
@@ -40,31 +40,29 @@
 #include <stdio.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/units.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/xtcio.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/tools/compare.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "compare.h"
-
 typedef struct {
     int bStep;
     int bTime;
diff --git a/src/gromacs/tools/compare.c b/src/gromacs/tools/compare.c
index 7dfe7a93d6..e2ee20b871 100644
--- a/src/gromacs/tools/compare.c
+++ b/src/gromacs/tools/compare.c
@@ -40,17 +40,18 @@
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/legacyheaders/names.h"
+
+#include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void cmp_int(FILE *fp, const char *s, int index, int i1, int i2)
 {
diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.c
index 814f7ee1e4..deaa798fce 100644
--- a/src/gromacs/tools/convert_tpr.c
+++ b/src/gromacs/tools/convert_tpr.c
@@ -38,25 +38,24 @@
 
 #include <math.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/state.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/gmxpreprocess/readir.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/utility/futil.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 #define RANGECHK(i, n) if ((i) >= (n)) gmx_fatal(FARGS, "Your index file contains atomnumbers (e.g. %d)\nthat are larger than the number of atoms in the tpr file (%d)", (i), (n))
diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.c
index 9c57a293d4..302ce26525 100644
--- a/src/gromacs/tools/dump.c
+++ b/src/gromacs/tools/dump.c
@@ -36,13 +36,13 @@
  */
 #include "gmxpre.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
diff --git a/src/gromacs/topology/atomprop.cpp b/src/gromacs/topology/atomprop.cpp
index 864c285590..a2fdfece3e 100644
--- a/src/gromacs/topology/atomprop.cpp
+++ b/src/gromacs/topology/atomprop.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/atomprop.h"
+#include "atomprop.h"
 
 #include <ctype.h>
 #include <string.h>
diff --git a/src/gromacs/topology/atomprop.h b/src/gromacs/topology/atomprop.h
index 33b0c60da8..5723123ac7 100644
--- a/src/gromacs/topology/atomprop.h
+++ b/src/gromacs/topology/atomprop.h
@@ -37,8 +37,8 @@
 #ifndef GMX_TOPOLOGY_ATOMPROP_H
 #define GMX_TOPOLOGY_ATOMPROP_H
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/topology/atoms.cpp b/src/gromacs/topology/atoms.cpp
index 0f4fada235..9d084240c2 100644
--- a/src/gromacs/topology/atoms.cpp
+++ b/src/gromacs/topology/atoms.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/atoms.h"
+#include "atoms.h"
 
 #include <cstring>
 
diff --git a/src/gromacs/topology/atoms.h b/src/gromacs/topology/atoms.h
index 4a619b0eb7..ed8d96c2ae 100644
--- a/src/gromacs/topology/atoms.h
+++ b/src/gromacs/topology/atoms.h
@@ -37,8 +37,8 @@
 #ifndef GMX_TOPOLOGY_ATOMS_H
 #define GMX_TOPOLOGY_ATOMS_H
 
-#include "../utility/basedefinitions.h"
-#include "../utility/real.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/topology/block.cpp b/src/gromacs/topology/block.cpp
index 9acf7ebe29..c4b2e51c27 100644
--- a/src/gromacs/topology/block.cpp
+++ b/src/gromacs/topology/block.cpp
@@ -36,8 +36,9 @@
  */
 #include "gmxpre.h"
 
+#include "block.h"
+
 #include <algorithm>
-#include "gromacs/topology/block.h"
 
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/topology/block.h b/src/gromacs/topology/block.h
index 599a4bd901..a3680e1a62 100644
--- a/src/gromacs/topology/block.h
+++ b/src/gromacs/topology/block.h
@@ -37,7 +37,7 @@
 #ifndef GMX_TOPOLOGY_BLOCK_H
 #define GMX_TOPOLOGY_BLOCK_H
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/topology/idef.h b/src/gromacs/topology/idef.h
index 00ce01cd6d..aaac95175f 100644
--- a/src/gromacs/topology/idef.h
+++ b/src/gromacs/topology/idef.h
@@ -37,7 +37,7 @@
 #ifndef GMX_TOPOLOGY_IDEF_H
 #define GMX_TOPOLOGY_IDEF_H
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/topology/index.cpp b/src/gromacs/topology/index.cpp
index 615c38a1bf..153554d900 100644
--- a/src/gromacs/topology/index.cpp
+++ b/src/gromacs/topology/index.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/index.h"
+#include "index.h"
 
 #include <assert.h>
 #include <ctype.h>
@@ -45,11 +45,10 @@
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/txtdump.h"
-
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/invblock.h"
diff --git a/src/gromacs/topology/index.h b/src/gromacs/topology/index.h
index 4bba1f8021..e361be73d5 100644
--- a/src/gromacs/topology/index.h
+++ b/src/gromacs/topology/index.h
@@ -39,7 +39,7 @@
 
 #include <stdio.h>
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/topology/invblock.c b/src/gromacs/topology/invblock.c
index c41dd0c0f8..48107b2c5f 100644
--- a/src/gromacs/topology/invblock.c
+++ b/src/gromacs/topology/invblock.c
@@ -37,10 +37,9 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/topology/invblock.h"
+#include "invblock.h"
 
 #include "gromacs/legacyheaders/types/simple.h"
-
 #include "gromacs/topology/block.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/topology/invblock.h b/src/gromacs/topology/invblock.h
index a3c79c7edd..f30e98a957 100644
--- a/src/gromacs/topology/invblock.h
+++ b/src/gromacs/topology/invblock.h
@@ -37,7 +37,7 @@
 #ifndef GMX_TOPOLOGY_INVBLOCK_H
 #define GMX_TOPOLOGY_INVBLOCK_H
 
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/topology/mtop_util.c b/src/gromacs/topology/mtop_util.c
index 622d4e46fe..b069c64419 100644
--- a/src/gromacs/topology/mtop_util.c
+++ b/src/gromacs/topology/mtop_util.c
@@ -34,14 +34,13 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/mtop_util.h"
+#include "mtop_util.h"
 
 #include <stdlib.h>
 #include <string.h>
 
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
-
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
diff --git a/src/gromacs/topology/mtop_util.h b/src/gromacs/topology/mtop_util.h
index a0cfef1aff..308476ea76 100644
--- a/src/gromacs/topology/mtop_util.h
+++ b/src/gromacs/topology/mtop_util.h
@@ -37,8 +37,8 @@
 #ifndef GMX_TOPOLOGY_MTOP_UTIL_H
 #define GMX_TOPOLOGY_MTOP_UTIL_H
 
-#include "../legacyheaders/types/inputrec.h"
-#include "../utility/basedefinitions.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/topology/residuetypes.cpp b/src/gromacs/topology/residuetypes.cpp
index 5bf67099a3..6745c96d37 100644
--- a/src/gromacs/topology/residuetypes.cpp
+++ b/src/gromacs/topology/residuetypes.cpp
@@ -34,7 +34,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/residuetypes.h"
+#include "residuetypes.h"
 
 #include <cassert>
 #include <cstdio>
diff --git a/src/gromacs/topology/symtab.cpp b/src/gromacs/topology/symtab.cpp
index 35134a5134..678088f478 100644
--- a/src/gromacs/topology/symtab.cpp
+++ b/src/gromacs/topology/symtab.cpp
@@ -44,7 +44,6 @@
 #include <algorithm>
 
 #include "gromacs/legacyheaders/txtdump.h"
-
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/topology/topology.cpp b/src/gromacs/topology/topology.cpp
index e554a94240..e5ff05371d 100644
--- a/src/gromacs/topology/topology.cpp
+++ b/src/gromacs/topology/topology.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/topology.h"
+#include "topology.h"
 
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/topology/topology.h b/src/gromacs/topology/topology.h
index b961fd932f..6f4e4792d4 100644
--- a/src/gromacs/topology/topology.h
+++ b/src/gromacs/topology/topology.h
@@ -37,11 +37,11 @@
 #ifndef GMX_TOPOLOGY_TOPOLOGY_H
 #define GMX_TOPOLOGY_TOPOLOGY_H
 
-#include "../math/vectypes.h"
-#include "atoms.h"
-#include "block.h"
-#include "idef.h"
-#include "symtab.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/symtab.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/topology/topsort.c b/src/gromacs/topology/topsort.c
index 8f1a007831..1f87499166 100644
--- a/src/gromacs/topology/topsort.c
+++ b/src/gromacs/topology/topsort.c
@@ -36,12 +36,11 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/topology/topsort.h"
+#include "topsort.h"
 
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/types/ifunc.h"
-
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/trajectoryanalysis.h b/src/gromacs/trajectoryanalysis.h
index 3a33b0d2cb..a79edd567a 100644
--- a/src/gromacs/trajectoryanalysis.h
+++ b/src/gromacs/trajectoryanalysis.h
@@ -276,17 +276,16 @@
 #ifndef GMX_TRAJECTORYANALYSIS_H
 #define GMX_TRAJECTORYANALYSIS_H
 
-#include "analysisdata.h"
-#include "options.h"
-#include "selection.h"
-
-#include "fileio/trx.h"
-#include "selection/nbsearch.h"
-#include "topology/topology.h"
-#include "trajectoryanalysis/analysismodule.h"
-#include "trajectoryanalysis/analysissettings.h"
-#include "trajectoryanalysis/cmdlinerunner.h"
-#include "utility/arrayref.h"
-#include "utility/exceptions.h"
+#include "gromacs/analysisdata.h"
+#include "gromacs/options.h"
+#include "gromacs/selection.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/trajectoryanalysis/cmdlinerunner.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
 
 #endif
diff --git a/src/gromacs/trajectoryanalysis/analysismodule.cpp b/src/gromacs/trajectoryanalysis/analysismodule.cpp
index 01d73254f6..a64a95fec7 100644
--- a/src/gromacs/trajectoryanalysis/analysismodule.cpp
+++ b/src/gromacs/trajectoryanalysis/analysismodule.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "analysismodule.h"
 
 #include <utility>
 
diff --git a/src/gromacs/trajectoryanalysis/analysismodule.h b/src/gromacs/trajectoryanalysis/analysismodule.h
index af1cfbbf18..a3846214b7 100644
--- a/src/gromacs/trajectoryanalysis/analysismodule.h
+++ b/src/gromacs/trajectoryanalysis/analysismodule.h
@@ -49,8 +49,8 @@
 
 #include <boost/shared_ptr.hpp>
 
-#include "../selection/selection.h" // For gmx::SelectionList
-#include "../utility/common.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
 
 struct t_pbc;
 struct t_trxframe;
diff --git a/src/gromacs/trajectoryanalysis/analysissettings-impl.h b/src/gromacs/trajectoryanalysis/analysissettings-impl.h
index a19c73b0ab..b42defaaa6 100644
--- a/src/gromacs/trajectoryanalysis/analysissettings-impl.h
+++ b/src/gromacs/trajectoryanalysis/analysissettings-impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,10 +42,9 @@
 #ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_IMPL_H
 #define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_IMPL_H
 
-#include "analysissettings.h"
-
-#include "../analysisdata/modules/plot.h"
-#include "../options/timeunitmanager.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/trajectoryanalysis/analysissettings.h b/src/gromacs/trajectoryanalysis/analysissettings.h
index 7687fdf178..5d40d2ac83 100644
--- a/src/gromacs/trajectoryanalysis/analysissettings.h
+++ b/src/gromacs/trajectoryanalysis/analysissettings.h
@@ -43,9 +43,9 @@
 #ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
 #define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
 
-#include "../options/timeunitmanager.h"
-#include "../math/vectypes.h"
-#include "../utility/common.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/utility/common.h"
 
 struct t_topology;
 
diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index d826b870a8..60684c4019 100644
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
@@ -57,11 +57,12 @@
 #include "gromacs/selection/selectionoptionmanager.h"
 #include "gromacs/trajectoryanalysis/analysismodule.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
-#include "gromacs/trajectoryanalysis/runnercommon.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/gmxassert.h"
 
+#include "runnercommon.h"
+
 namespace gmx
 {
 
diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.h b/src/gromacs/trajectoryanalysis/cmdlinerunner.h
index 0b87455e85..242a629959 100644
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.h
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,8 +43,8 @@
 #ifndef GMX_TRAJECTORYANALYSIS_CMDLINERUNNER_H
 #define GMX_TRAJECTORYANALYSIS_CMDLINERUNNER_H
 
-#include "analysismodule.h"
-#include "../utility/common.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/trajectoryanalysis/modules.cpp b/src/gromacs/trajectoryanalysis/modules.cpp
index 423d585e82..07a3a8c378 100644
--- a/src/gromacs/trajectoryanalysis/modules.cpp
+++ b/src/gromacs/trajectoryanalysis/modules.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/trajectoryanalysis/modules.h"
+#include "modules.h"
 
 #include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/trajectoryanalysis/cmdlinerunner.h"
diff --git a/src/gromacs/trajectoryanalysis/modules/angle.h b/src/gromacs/trajectoryanalysis/modules/angle.h
index 80976ebca4..24b81c7356 100644
--- a/src/gromacs/trajectoryanalysis/modules/angle.h
+++ b/src/gromacs/trajectoryanalysis/modules/angle.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_ANGLE_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_ANGLE_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/trajectoryanalysis/modules/distance.h b/src/gromacs/trajectoryanalysis/modules/distance.h
index 7d354e3894..519176d577 100644
--- a/src/gromacs/trajectoryanalysis/modules/distance.h
+++ b/src/gromacs/trajectoryanalysis/modules/distance.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_DISTANCE_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_DISTANCE_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/trajectoryanalysis/modules/freevolume.cpp b/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
index 31785088a3..127a834b1b 100644
--- a/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
@@ -45,12 +45,11 @@
 
 #include <string>
 
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/modules/average.h"
 #include "gromacs/analysisdata/modules/plot.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"
diff --git a/src/gromacs/trajectoryanalysis/modules/freevolume.h b/src/gromacs/trajectoryanalysis/modules/freevolume.h
index cc96d6a8e6..ba24de0951 100644
--- a/src/gromacs/trajectoryanalysis/modules/freevolume.h
+++ b/src/gromacs/trajectoryanalysis/modules/freevolume.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_FREEVOLUME_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_FREEVOLUME_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/trajectoryanalysis/modules/sasa.cpp b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
index 015e1e043d..6fec3377ab 100644
--- a/src/gromacs/trajectoryanalysis/modules/sasa.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
@@ -49,14 +49,13 @@
 #include <string>
 #include <vector>
 
-#include "gromacs/legacyheaders/copyrite.h"
-
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/modules/average.h"
 #include "gromacs/analysisdata/modules/plot.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
diff --git a/src/gromacs/trajectoryanalysis/modules/sasa.h b/src/gromacs/trajectoryanalysis/modules/sasa.h
index dcf7329702..4e2ca5eb1e 100644
--- a/src/gromacs/trajectoryanalysis/modules/sasa.h
+++ b/src/gromacs/trajectoryanalysis/modules/sasa.h
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_SASA_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_SASA_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/trajectoryanalysis/modules/select.h b/src/gromacs/trajectoryanalysis/modules/select.h
index 90c4898fa3..62b26a34af 100644
--- a/src/gromacs/trajectoryanalysis/modules/select.h
+++ b/src/gromacs/trajectoryanalysis/modules/select.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
 #define GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
 
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/trajectoryanalysis/runnercommon.cpp b/src/gromacs/trajectoryanalysis/runnercommon.cpp
index bf610b3827..4d9513ed28 100644
--- a/src/gromacs/trajectoryanalysis/runnercommon.cpp
+++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp
@@ -45,12 +45,11 @@
 
 #include <string.h>
 
-#include "gromacs/legacyheaders/oenv.h"
-
 #include "gromacs/fileio/timecontrol.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"
diff --git a/src/gromacs/trajectoryanalysis/tests/angle.cpp b/src/gromacs/trajectoryanalysis/tests/angle.cpp
index 70a6aec5a3..94701813fb 100644
--- a/src/gromacs/trajectoryanalysis/tests/angle.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/angle.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/angle.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 
 #include "moduletest.h"
diff --git a/src/gromacs/trajectoryanalysis/tests/distance.cpp b/src/gromacs/trajectoryanalysis/tests/distance.cpp
index 2719c1a1b4..5a63636346 100644
--- a/src/gromacs/trajectoryanalysis/tests/distance.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/distance.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/distance.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 
 #include "moduletest.h"
diff --git a/src/gromacs/trajectoryanalysis/tests/freevolume.cpp b/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
index 4b85fd956f..f199976cc5 100644
--- a/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/freevolume.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 
 #include "moduletest.h"
diff --git a/src/gromacs/trajectoryanalysis/tests/sasa.cpp b/src/gromacs/trajectoryanalysis/tests/sasa.cpp
index 6a9c975900..75a60d69df 100644
--- a/src/gromacs/trajectoryanalysis/tests/sasa.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/sasa.cpp
@@ -54,10 +54,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/sasa.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 #include "testutils/testasserts.h"
 
diff --git a/src/gromacs/trajectoryanalysis/tests/select.cpp b/src/gromacs/trajectoryanalysis/tests/select.cpp
index 5232cc9e60..05a24a4707 100644
--- a/src/gromacs/trajectoryanalysis/tests/select.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/select.cpp
@@ -49,10 +49,10 @@
  */
 #include "gmxpre.h"
 
-#include <gtest/gtest.h>
-
 #include "gromacs/trajectoryanalysis/modules/select.h"
 
+#include <gtest/gtest.h>
+
 #include "testutils/cmdlinetest.h"
 
 #include "moduletest.h"
diff --git a/src/gromacs/utility.h b/src/gromacs/utility.h
index 9abfa1cbb6..a25f70cb10 100644
--- a/src/gromacs/utility.h
+++ b/src/gromacs/utility.h
@@ -160,10 +160,10 @@
 #ifndef GMX_UTILITY_H
 #define GMX_UTILITY_H
 
-#include "utility/errorcodes.h"
-#include "utility/exceptions.h"
-#include "utility/gmxassert.h"
-#include "utility/init.h"
-#include "utility/programcontext.h"
+#include "gromacs/utility/errorcodes.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/init.h"
+#include "gromacs/utility/programcontext.h"
 
 #endif
diff --git a/src/gromacs/utility/arrayref.h b/src/gromacs/utility/arrayref.h
index 982c712b7d..fb4778d24a 100644
--- a/src/gromacs/utility/arrayref.h
+++ b/src/gromacs/utility/arrayref.h
@@ -50,7 +50,7 @@
 #include <utility>
 #include <vector>
 
-#include "gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/utility/baseversion.cpp b/src/gromacs/utility/baseversion.cpp
index dff527782c..876dbeb5b1 100644
--- a/src/gromacs/utility/baseversion.cpp
+++ b/src/gromacs/utility/baseversion.cpp
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include "baseversion.h"
+
 #include "baseversion-gen.h"
 
 const char *gmx_version()
diff --git a/src/gromacs/utility/cstringutil.c b/src/gromacs/utility/cstringutil.c
index 85cbd41c0a..14f010c077 100644
--- a/src/gromacs/utility/cstringutil.c
+++ b/src/gromacs/utility/cstringutil.c
@@ -39,6 +39,8 @@
 
 #include "cstringutil.h"
 
+#include "config.h"
+
 #include <assert.h>
 #include <ctype.h>
 #include <stdio.h>
@@ -48,8 +50,6 @@
 
 #include <sys/types.h>
 
-#include "config.h"
-
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
diff --git a/src/gromacs/utility/cstringutil.h b/src/gromacs/utility/cstringutil.h
index a8b7460e4a..9bd8e3b85e 100644
--- a/src/gromacs/utility/cstringutil.h
+++ b/src/gromacs/utility/cstringutil.h
@@ -43,12 +43,12 @@
 #ifndef GMX_UTILITY_CSTRINGUTIL_H
 #define GMX_UTILITY_CSTRINGUTIL_H
 
+#include "gromacs/utility/gmx_header_config.h"
+
 #include <stdio.h>
 #include <time.h>
 
-#include "basedefinitions.h"
-
-#include "gmx_header_config.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/utility/errorcodes.cpp b/src/gromacs/utility/errorcodes.cpp
index 4d513a1365..00c57aa67c 100644
--- a/src/gromacs/utility/errorcodes.cpp
+++ b/src/gromacs/utility/errorcodes.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/errorcodes.h"
+#include "errorcodes.h"
 
 #include <cstdlib>
 
diff --git a/src/gromacs/utility/errorformat.cpp b/src/gromacs/utility/errorformat.cpp
index a5ba90bf01..a8f7159c29 100644
--- a/src/gromacs/utility/errorformat.cpp
+++ b/src/gromacs/utility/errorformat.cpp
@@ -41,10 +41,10 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include "errorformat.h"
 
+#include "config.h"
+
 #include <cctype>
 #include <cstdio>
 #include <cstring>
diff --git a/src/gromacs/utility/exceptions.cpp b/src/gromacs/utility/exceptions.cpp
index 5ccd830707..952383ffad 100644
--- a/src/gromacs/utility/exceptions.cpp
+++ b/src/gromacs/utility/exceptions.cpp
@@ -51,8 +51,8 @@
 #include <stdexcept>
 #include <typeinfo>
 
-#include <boost/exception/get_error_info.hpp>
 #include <boost/shared_ptr.hpp>
+#include <boost/exception/get_error_info.hpp>
 
 #include "thread_mpi/system_error.h"
 
diff --git a/src/gromacs/utility/exceptions.h b/src/gromacs/utility/exceptions.h
index ace7b66224..e6a8929320 100644
--- a/src/gromacs/utility/exceptions.h
+++ b/src/gromacs/utility/exceptions.h
@@ -51,11 +51,11 @@
 #include <vector>
 
 #include <boost/exception_ptr.hpp>
+#include <boost/throw_exception.hpp>
 #include <boost/exception/errinfo_api_function.hpp>
 #include <boost/exception/errinfo_errno.hpp>
 #include <boost/exception/exception.hpp>
 #include <boost/exception/info.hpp>
-#include <boost/throw_exception.hpp>
 
 namespace gmx
 {
diff --git a/src/gromacs/utility/fatalerror.h b/src/gromacs/utility/fatalerror.h
index 7d380bc419..1dd4cff339 100644
--- a/src/gromacs/utility/fatalerror.h
+++ b/src/gromacs/utility/fatalerror.h
@@ -47,7 +47,7 @@
 #include <stdarg.h>
 #include <stdio.h>
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/utility/file.cpp b/src/gromacs/utility/file.cpp
index 31055f28b8..174fa00803 100644
--- a/src/gromacs/utility/file.cpp
+++ b/src/gromacs/utility/file.cpp
@@ -43,6 +43,8 @@
 
 #include "file.h"
 
+#include "config.h"
+
 #include <cerrno>
 #include <cstdio>
 #include <cstring>
@@ -53,8 +55,6 @@
 
 #include <sys/stat.h>
 
-#include "config.h"
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
diff --git a/src/gromacs/utility/file.h b/src/gromacs/utility/file.h
index 15b48d16a5..ef837b4a84 100644
--- a/src/gromacs/utility/file.h
+++ b/src/gromacs/utility/file.h
@@ -47,7 +47,7 @@
 
 #include <string>
 
-#include "common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/utility/futil.cpp b/src/gromacs/utility/futil.cpp
index af28843ef5..546b875808 100644
--- a/src/gromacs/utility/futil.cpp
+++ b/src/gromacs/utility/futil.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/futil.h"
+#include "futil.h"
 
 #include "config.h"
 
@@ -44,9 +44,9 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include <sys/types.h>
-#include <sys/stat.h>
 #include <fcntl.h>
+#include <sys/stat.h>
+#include <sys/types.h>
 
 #ifdef HAVE_DIRENT_H
 /* POSIX */
@@ -58,9 +58,9 @@
 #endif
 
 #ifdef GMX_NATIVE_WINDOWS
-#include <windows.h>
 #include <direct.h>
 #include <io.h>
+#include <windows.h>
 #endif
 
 /* Windows file stuff, only necessary for visual studio */
diff --git a/src/gromacs/utility/futil.h b/src/gromacs/utility/futil.h
index 9f94773016..8e669e09d3 100644
--- a/src/gromacs/utility/futil.h
+++ b/src/gromacs/utility/futil.h
@@ -48,7 +48,7 @@
 #include <limits.h>
 #include <stdio.h>
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -57,7 +57,7 @@ extern "C" {
 }
 #endif
 
-#include "gmx_header_config.h"
+#include "gromacs/utility/gmx_header_config.h"
 /*! \def DIR_SEPARATOR
  * \brief
  * Directory separator on this OS.
diff --git a/src/gromacs/utility/gmxassert.h b/src/gromacs/utility/gmxassert.h
index b47d9d0933..a919080d32 100644
--- a/src/gromacs/utility/gmxassert.h
+++ b/src/gromacs/utility/gmxassert.h
@@ -45,7 +45,7 @@
 
 #include <boost/current_function.hpp>
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 //! \addtogroup module_utility
 //! \{
diff --git a/src/gromacs/utility/gmxmpi.h b/src/gromacs/utility/gmxmpi.h
index bb6570cdfa..cacc0a0cbe 100644
--- a/src/gromacs/utility/gmxmpi.h
+++ b/src/gromacs/utility/gmxmpi.h
@@ -73,8 +73,8 @@
 #endif /*MPI_INT64_T*/
 #else
 #ifdef GMX_THREAD_MPI
-#include "thread_mpi/tmpi.h"
 #include "thread_mpi/mpi_bindings.h"
+#include "thread_mpi/tmpi.h"
 #else
 typedef void* MPI_Comm;
 typedef void* MPI_Request;
diff --git a/src/gromacs/utility/gmxomp.cpp b/src/gromacs/utility/gmxomp.cpp
index 04abd12a8e..15989a16fe 100644
--- a/src/gromacs/utility/gmxomp.cpp
+++ b/src/gromacs/utility/gmxomp.cpp
@@ -40,7 +40,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/gmxomp.h"
+#include "gmxomp.h"
 
 #include "config.h"
 
diff --git a/src/gromacs/utility/gmxomp.h b/src/gromacs/utility/gmxomp.h
index f0e67a593f..553eadc092 100644
--- a/src/gromacs/utility/gmxomp.h
+++ b/src/gromacs/utility/gmxomp.h
@@ -67,7 +67,7 @@
 #include <windows.h>
 #endif
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C"
diff --git a/src/gromacs/utility/gmxregex.h b/src/gromacs/utility/gmxregex.h
index a80f523bee..9385163082 100644
--- a/src/gromacs/utility/gmxregex.h
+++ b/src/gromacs/utility/gmxregex.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@
 
 #include <string>
 
-#include "common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/utility/init.cpp b/src/gromacs/utility/init.cpp
index 3fbc8c554c..f211053574 100644
--- a/src/gromacs/utility/init.cpp
+++ b/src/gromacs/utility/init.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/init.h"
+#include "init.h"
 
 #include "config.h"
 
diff --git a/src/gromacs/utility/messagestringcollector.cpp b/src/gromacs/utility/messagestringcollector.cpp
index 9d631acbce..937bb541cb 100644
--- a/src/gromacs/utility/messagestringcollector.cpp
+++ b/src/gromacs/utility/messagestringcollector.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/messagestringcollector.h"
+#include "messagestringcollector.h"
 
 #include <vector>
 
diff --git a/src/gromacs/utility/messagestringcollector.h b/src/gromacs/utility/messagestringcollector.h
index aca59a33b1..b78af98447 100644
--- a/src/gromacs/utility/messagestringcollector.h
+++ b/src/gromacs/utility/messagestringcollector.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@
 
 #include <string>
 
-#include "../utility/common.h"
+#include "gromacs/utility/common.h"
 
 namespace gmx
 {
diff --git a/src/gromacs/utility/path.cpp b/src/gromacs/utility/path.cpp
index 0a0e54bc76..1302d30f97 100644
--- a/src/gromacs/utility/path.cpp
+++ b/src/gromacs/utility/path.cpp
@@ -43,6 +43,8 @@
 
 #include "path.h"
 
+#include "config.h"
+
 #include <cctype>
 #include <cerrno>
 #include <cstdlib>
@@ -52,8 +54,6 @@
 
 #include <sys/stat.h>
 
-#include "config.h"
-
 #ifdef GMX_NATIVE_WINDOWS
 #include <direct.h>
 #else
diff --git a/src/gromacs/utility/programcontext.cpp b/src/gromacs/utility/programcontext.cpp
index 5b73060158..ac9bc13dd7 100644
--- a/src/gromacs/utility/programcontext.cpp
+++ b/src/gromacs/utility/programcontext.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/programcontext.h"
+#include "programcontext.h"
 
 #include <cstddef>
 
diff --git a/src/gromacs/utility/scoped_ptr_sfree.h b/src/gromacs/utility/scoped_ptr_sfree.h
index 3c1077ccae..7078a80aeb 100644
--- a/src/gromacs/utility/scoped_ptr_sfree.h
+++ b/src/gromacs/utility/scoped_ptr_sfree.h
@@ -43,7 +43,7 @@
 #ifndef GMX_UTILITY_SCOPED_PTR_SFREE_H
 #define GMX_UTILITY_SCOPED_PTR_SFREE_H
 
-#include "common.h"
+#include "gromacs/utility/common.h"
 #include "gromacs/utility/smalloc.h"
 
 namespace gmx
diff --git a/src/gromacs/utility/smalloc.c b/src/gromacs/utility/smalloc.c
index e542c55327..16d70514b9 100644
--- a/src/gromacs/utility/smalloc.c
+++ b/src/gromacs/utility/smalloc.c
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
+#include "smalloc.h"
 
 #include "config.h"
 
diff --git a/src/gromacs/utility/smalloc.h b/src/gromacs/utility/smalloc.h
index 91e2ebe89e..74d71a5586 100644
--- a/src/gromacs/utility/smalloc.h
+++ b/src/gromacs/utility/smalloc.h
@@ -73,7 +73,7 @@
 
 #include <stddef.h>
 
-#include "basedefinitions.h"
+#include "gromacs/utility/basedefinitions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/utility/stringutil.cpp b/src/gromacs/utility/stringutil.cpp
index 3f33caeb1d..5b2c725017 100644
--- a/src/gromacs/utility/stringutil.cpp
+++ b/src/gromacs/utility/stringutil.cpp
@@ -44,8 +44,8 @@
 #include "stringutil.h"
 
 #include <cctype>
-#include <cstdio>
 #include <cstdarg>
+#include <cstdio>
 #include <cstring>
 
 #include <algorithm>
diff --git a/src/gromacs/utility/tests/stringutil.cpp b/src/gromacs/utility/tests/stringutil.cpp
index c63a9c4559..dcdc5cba0c 100644
--- a/src/gromacs/utility/tests/stringutil.cpp
+++ b/src/gromacs/utility/tests/stringutil.cpp
@@ -45,14 +45,14 @@
  */
 #include "gmxpre.h"
 
+#include "gromacs/utility/stringutil.h"
+
 #include <string>
 #include <vector>
 
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/utility/stringutil.h"
-
 #include "testutils/refdata.h"
 #include "testutils/stringtest.h"