#include "gmxpre.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.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/smalloc.h"
const char *desc[] = {
"[THISMODULE] analyzes solvent orientation around solutes.",
"It calculates two angles between the vector from one or more",
- "reference positions to the first atom of each solvent molecule:[PAR]",
- "[GRK]theta[grk][SUB]1[sub]: the angle with the vector from the first atom of the solvent",
- "molecule to the midpoint between atoms 2 and 3.[BR]",
- "[GRK]theta[grk][SUB]2[sub]: the angle with the normal of the solvent plane, defined by the",
- "same three atoms, or, when the option [TT]-v23[tt] is set, ",
- "the angle with the vector between atoms 2 and 3.[PAR]",
+ "reference positions to the first atom of each solvent molecule:",
+ "",
+ " * [GRK]theta[grk][SUB]1[sub]: the angle with the vector from the first atom of the solvent",
+ " molecule to the midpoint between atoms 2 and 3.",
+ " * [GRK]theta[grk][SUB]2[sub]: the angle with the normal of the solvent plane, defined by the",
+ " same three atoms, or, when the option [TT]-v23[tt] is set, ",
+ " the angle with the vector between atoms 2 and 3.",
+ "",
"The reference can be a set of atoms or",
"the center of mass of a set of atoms. The group of solvent atoms should",
"consist of 3 atoms per solvent molecule.",