#include <stdlib.h>
#include <string.h>
#include <time.h>
+
#include "typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/mdlib/groupcoord.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
#include "macros.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "names.h"
#include "network.h"
#include "mdrun.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "copyrite.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/timing/wallcycle.h"
#include "swapcoords.h"
+#include "gromacs/pbcutil/pbc.h"
+
static char *SwS = {"SWAP:"}; /**< For output that comes from the swap module */
static char *SwSEmpty = {" "}; /**< Placeholder for multi-line output */
static char* IonString[eIonNR] = {"anion", "cation" }; /**< Type of ion, used for verbose output */