From b4a6e67ea25f01007e0f008861d8659cec01d2c9 Mon Sep 17 00:00:00 2001
From: Justin Lemkul <jalemkul@vt.edu>
Date: Sun, 23 Jan 2011 19:01:08 -0500
Subject: [PATCH] Various small changes to the man pages.

---
 src/tools/g_anadock.c     | 2 +-
 src/tools/g_sigeps.c      | 2 +-
 src/tools/gmx_cluster.c   | 2 +-
 src/tools/gmx_density.c   | 2 +-
 src/tools/gmx_disre.c     | 4 ++--
 src/tools/gmx_energy.c    | 6 +++---
 src/tools/gmx_filter.c    | 2 +-
 src/tools/gmx_h2order.c   | 8 ++++----
 src/tools/gmx_kinetics.c  | 2 +-
 src/tools/gmx_nmeig.c     | 6 +++---
 src/tools/gmx_nmens.c     | 2 +-
 src/tools/gmx_nmtraj.c    | 8 ++++----
 src/tools/gmx_potential.c | 2 +-
 src/tools/gmx_rmsf.c      | 2 +-
 src/tools/gmx_rotacf.c    | 7 ++-----
 src/tools/gmx_saltbr.c    | 2 +-
 16 files changed, 28 insertions(+), 31 deletions(-)

diff --git a/src/tools/g_anadock.c b/src/tools/g_anadock.c
index 713d7fd563..e7c7861c60 100644
--- a/src/tools/g_anadock.c
+++ b/src/tools/g_anadock.c
@@ -301,7 +301,7 @@ int main(int argc,char *argv[])
     "and free energy estimates are analysed, and for each cluster the",
     "energy statistics are printed.[PAR]",
     "An alternative approach to this is to cluster the structures first",
-    "(using [TT]g_cluster[tt] and then sort the clusters on either lowest",
+    "using [TT]g_cluster[tt] and then sort the clusters on either lowest",
     "energy or average energy."
   };
   t_filenm fnm[] = {
diff --git a/src/tools/g_sigeps.c b/src/tools/g_sigeps.c
index 1527456dea..9737220d75 100644
--- a/src/tools/g_sigeps.c
+++ b/src/tools/g_sigeps.c
@@ -73,7 +73,7 @@ real dpot(real x,real qq,real c6,real cn,int npow)
 int main(int argc,char *argv[])
 {
   const char *desc[] = {
-    "g_sigeps is a simple utility that converts c6/c12 or c6/cn combinations",
+    "[TT]g_sigeps[tt] is a simple utility that converts c6/c12 or c6/cn combinations",
     "to sigma and epsilon, or vice versa. It can also plot the potential",
     "in  file. In addition it makes an approximation of a Buckingham potential",
     "to a Lennard Jones potential."
diff --git a/src/tools/gmx_cluster.c b/src/tools/gmx_cluster.c
index ecd778b33e..bf1452846e 100644
--- a/src/tools/gmx_cluster.c
+++ b/src/tools/gmx_cluster.c
@@ -953,7 +953,7 @@ int gmx_cluster(int argc,char *argv[])
   const char *desc[] = {
     "[TT]g_cluster[tt] can cluster structures with several different methods.",
     "Distances between structures can be determined from a trajectory",
-    "or read from an XPM matrix file with the [TT]-dm[tt] option.",
+    "or read from an [TT].xpm[tt] matrix file with the [TT]-dm[tt] option.",
     "RMS deviation after fitting or RMS deviation of atom-pair distances",
     "can be used to define the distance between structures.[PAR]",
     
diff --git a/src/tools/gmx_density.c b/src/tools/gmx_density.c
index 776fe02a02..20be2290d6 100644
--- a/src/tools/gmx_density.c
+++ b/src/tools/gmx_density.c
@@ -368,7 +368,7 @@ int gmx_density(int argc,char *argv[])
     "Compute partial densities across the box, using an index file.[PAR]",
     "For the total density of NPT simulations, use [TT]g_energy[tt] instead.",
     "[PAR]",
-    "Densities in kg/m^3, number densities or electron densities can be",
+    "Densities are in kg/m^3, and number densities or electron densities can also be",
     "calculated. For electron densities, a file describing the number of",
     "electrons for each type of atom should be provided using [TT]-ei[tt].",
     "It should look like:[BR]",
diff --git a/src/tools/gmx_disre.c b/src/tools/gmx_disre.c
index 21864f04e7..a750da7638 100644
--- a/src/tools/gmx_disre.c
+++ b/src/tools/gmx_disre.c
@@ -544,8 +544,8 @@ int gmx_disre(int argc,char *argv[])
 {
   const char *desc[] = {
     "[TT]g_disre[tt] computes violations of distance restraints.",
-    "If necessary all protons can be added to a protein molecule ",
-    "using the protonate program.[PAR]",
+    "If necessary, all protons can be added to a protein molecule ",
+    "using the [TT]g_protonate[tt] program.[PAR]",
     "The program always",
     "computes the instantaneous violations rather than time-averaged,",
     "because this analysis is done from a trajectory file afterwards",
diff --git a/src/tools/gmx_energy.c b/src/tools/gmx_energy.c
index 78c8526fa3..b84ab3034b 100644
--- a/src/tools/gmx_energy.c
+++ b/src/tools/gmx_energy.c
@@ -1510,7 +1510,7 @@ int gmx_energy(int argc,char *argv[])
     
     "Average, RMSD and drift are calculated with full precision from the",
     "simulation (see printed manual). Drift is calculated by performing",
-    "a LSQ fit of the data to a straight line. The reported total drift",
+    "a least-squares fit of the data to a straight line. The reported total drift",
     "is the difference of the fit at the first and last point.",
     "An error estimate of the average is given based on a block averages",
     "over 5 blocks using the full precision averages. The error estimate",
@@ -1520,10 +1520,10 @@ int gmx_energy(int argc,char *argv[])
     "MD steps, or over many more points than the number of frames in",
     "energy file. This makes the [TT]g_energy[tt] statistics output more accurate",
     "than the [TT].xvg[tt] output. When exact averages are not present in the energy",
-    "file the statistics mentioned above is simply over the single, per-frame",
+    "file the statistics mentioned above are simply over the single, per-frame",
     "energy values.[PAR]",
 
-    "The term fluctuation gives the RMSD around the LSQ fit.[PAR]",
+    "The term fluctuation gives the RMSD around the least-squares fit.[PAR]",
     
     "Some fluctuation-dependent properties can be calculated provided",
     "the correct energy terms are selected. The following properties",
diff --git a/src/tools/gmx_filter.c b/src/tools/gmx_filter.c
index 914bf0e7a3..95646e95e7 100644
--- a/src/tools/gmx_filter.c
+++ b/src/tools/gmx_filter.c
@@ -76,7 +76,7 @@ int gmx_filter(int argc,char *argv[])
     "Option [TT]-oh[tt] writes a high-pass filtered trajectory.",
     "The high-pass filtered coordinates are added to the coordinates",
     "from the structure file. When using high-pass filtering use [TT]-fit[tt]",
-    "or make sure you use a trajectory which has been fitted on",
+    "or make sure you use a trajectory that has been fitted on",
     "the coordinates in the structure file."
   };
   
diff --git a/src/tools/gmx_h2order.c b/src/tools/gmx_h2order.c
index f8313d6a6a..1785fea7b8 100644
--- a/src/tools/gmx_h2order.c
+++ b/src/tools/gmx_h2order.c
@@ -246,7 +246,7 @@ void h2order_plot(rvec dipole[], real order[], const char *afile,
 int gmx_h2order(int argc,char *argv[])
 {
   const char *desc[] = {
-    "Compute the orientation of water molecules with respect to the normal",
+    "[TT]g_h2order[tt] computes the orientation of water molecules with respect to the normal",
     "of the box. The program determines the average cosine of the angle",
     "between the dipole moment of water and an axis of the box. The box is",
     "divided in slices and the average orientation per slice is printed.",
@@ -266,9 +266,9 @@ int gmx_h2order(int argc,char *argv[])
       " in #nr slices."}
   };
   const char *bugs[] = {
-    "The program assigns whole water molecules to a slice, based on the first"
-    "atom of three in the index file group. It assumes an order O,H,H."
-    "Name is not important, but the order is. If this demand is not met,"
+    "The program assigns whole water molecules to a slice, based on the first "
+    "atom of three in the index file group. It assumes an order O,H,H. "
+    "Name is not important, but the order is. If this demand is not met, "
     "assigning molecules to slices is different."
   };
 
diff --git a/src/tools/gmx_kinetics.c b/src/tools/gmx_kinetics.c
index 1312304ce8..562c6b3043 100644
--- a/src/tools/gmx_kinetics.c
+++ b/src/tools/gmx_kinetics.c
@@ -668,7 +668,7 @@ static void dump_remd_parameters(FILE *gp,t_remd_data *d,const char *fn,
 int gmx_kinetics(int argc,char *argv[])
 {
   const char *desc[] = {
-    "g_kinetics reads two [TT].xvg[tt] files, each one containing data for N replicas.",
+    "[TT]g_kinetics[tt] reads two [TT].xvg[tt] files, each one containing data for N replicas.",
     "The first file contains the temperature of each replica at each timestep,",
     "and the second contains real values that can be interpreted as",
     "an indicator for folding. If the value in the file is larger than",
diff --git a/src/tools/gmx_nmeig.c b/src/tools/gmx_nmeig.c
index 9e43fdaaeb..64f95e0fe5 100644
--- a/src/tools/gmx_nmeig.c
+++ b/src/tools/gmx_nmeig.c
@@ -196,9 +196,9 @@ int gmx_nmeig(int argc,char *argv[])
     "The eigenvectors can be analyzed with [TT]g_anaeig[tt].",
     "An ensemble of structures can be generated from the eigenvectors with",
     "[TT]g_nmens[tt]. When mass weighting is used, the generated eigenvectors",
-    "will be scaled back to plain cartesian coordinates before generating the",
-    "output - in this case they will no longer be exactly orthogonal in the",
-    "standard cartesian norm (But in the mass weighted norm they would be)."
+    "will be scaled back to plain Cartesian coordinates before generating the",
+    "output. In this case, they will no longer be exactly orthogonal in the",
+    "standard Cartesian norm, but in the mass-weighted norm they would be."
   };
     
   static gmx_bool bM=TRUE;
diff --git a/src/tools/gmx_nmens.c b/src/tools/gmx_nmens.c
index 0c069daf3e..3a925e54cd 100644
--- a/src/tools/gmx_nmens.c
+++ b/src/tools/gmx_nmens.c
@@ -63,7 +63,7 @@ int gmx_nmens(int argc,char *argv[])
 {
   const char *desc[] = {
     "[TT]g_nmens[tt] generates an ensemble around an average structure",
-    "in a subspace which is defined by a set of normal modes (eigenvectors).",
+    "in a subspace that is defined by a set of normal modes (eigenvectors).",
     "The eigenvectors are assumed to be mass-weighted.",
     "The position along each eigenvector is randomly taken from a Gaussian",
     "distribution with variance kT/eigenvalue.[PAR]",
diff --git a/src/tools/gmx_nmtraj.c b/src/tools/gmx_nmtraj.c
index e26f5b1ca3..8362a27b36 100644
--- a/src/tools/gmx_nmtraj.c
+++ b/src/tools/gmx_nmtraj.c
@@ -64,7 +64,7 @@ int gmx_nmtraj(int argc,char *argv[])
     const char *desc[] = 
     {
         "[TT]g_nmtraj[tt] generates an virtual trajectory from an eigenvector, ",
-        "corresponding to a harmonic cartesian oscillation around the average ",
+        "corresponding to a harmonic Cartesian oscillation around the average ",
         "structure. The eigenvectors should normally be mass-weighted, but you can ",
         "use non-weighted eigenvectors to generate orthogonal motions. ",
         "The output frames are written as a trajectory file covering an entire period, and ",
@@ -72,10 +72,10 @@ int gmx_nmtraj(int argc,char *argv[])
         "PDB format you can view it directly in PyMol and also render a photorealistic movie. ",
         "Motion amplitudes are calculated from the eigenvalues and a preset temperature, ",
         "assuming equipartition of the energy over all modes. To make the motion clearly visible ",
-        "in PyMol you might want to amplify it by setting an unrealistic high temperature. ", 
-        "However, be aware that both the linear cartesian displacements and mass weighting will ",
+        "in PyMol you might want to amplify it by setting an unrealistically high temperature. ", 
+        "However, be aware that both the linear Cartesian displacements and mass weighting will ",
         "lead to serious structure deformation for high amplitudes - this is is simply a limitation ",
-        "of the cartesian normal mode model. By default the selected eigenvector is set to 7, since ",
+        "of the Cartesian normal mode model. By default the selected eigenvector is set to 7, since ",
         " the first six normal modes are the translational and rotational degrees of freedom." 
     };
 
diff --git a/src/tools/gmx_potential.c b/src/tools/gmx_potential.c
index 34a67582ce..c674551974 100644
--- a/src/tools/gmx_potential.c
+++ b/src/tools/gmx_potential.c
@@ -387,7 +387,7 @@ void plot_potential(double *potential[], double *charge[], double *field[],
 int gmx_potential(int argc,char *argv[])
 {
   const char *desc[] = {
-    "Compute the electrostatical potential across the box. The potential is",
+    "[TT]g_potential[tt] computes the electrostatical potential across the box. The potential is",
     "calculated by first summing the charges per slice and then integrating",
     "twice of this charge distribution. Periodic boundaries are not taken",
     "into account. Reference of potential is taken to be the left side of",
diff --git a/src/tools/gmx_rmsf.c b/src/tools/gmx_rmsf.c
index d983bf7e7a..71307c66e4 100644
--- a/src/tools/gmx_rmsf.c
+++ b/src/tools/gmx_rmsf.c
@@ -180,7 +180,7 @@ int gmx_rmsf(int argc,char *argv[])
     "temperature factors and then it will also output average coordinates",
     "and a [TT].pdb[tt] file with ANISOU records (corresonding to the [TT]-oq[tt]",
     "or [TT]-ox[tt] option). Please note that the U values",
-    "are orientation dependent, so before comparison with experimental data",
+    "are orientation-dependent, so before comparison with experimental data",
     "you should verify that you fit to the experimental coordinates.[PAR]",
     "When a [TT].pdb[tt] input file is passed to the program and the [TT]-aniso[tt]",
     "flag is set",
diff --git a/src/tools/gmx_rotacf.c b/src/tools/gmx_rotacf.c
index 5d9d7c121e..76d7bf48b2 100644
--- a/src/tools/gmx_rotacf.c
+++ b/src/tools/gmx_rotacf.c
@@ -59,7 +59,7 @@ int gmx_rotacf(int argc,char *argv[])
   const char *desc[] = {
     "[TT]g_rotacf[tt] calculates the rotational correlation function",
     "for molecules. Three atoms (i,j,k) must be given in the index",
-    "file, defining two vectors ij and jk. The rotational acf",
+    "file, defining two vectors ij and jk. The rotational ACF",
     "is calculated as the autocorrelation function of the vector",
     "n = ij x jk, i.e. the cross product of the two vectors.",
     "Since three atoms span a plane, the order of the three atoms",
@@ -73,10 +73,7 @@ int gmx_rotacf(int argc,char *argv[])
     "This will calculate the rotational correlation function using a first",
     "order Legendre polynomial of the angle of a vector defined by the index",
     "file. The correlation function will be fitted from 2.5 ps until 20.0 ps",
-    "to a two parameter exponential.",
-
-
-    ""
+    "to a two-parameter exponential."
   };
   static gmx_bool bVec    = FALSE,bAver=TRUE;
 
diff --git a/src/tools/gmx_saltbr.c b/src/tools/gmx_saltbr.c
index 2431c1dc75..9c5ee3c928 100644
--- a/src/tools/gmx_saltbr.c
+++ b/src/tools/gmx_saltbr.c
@@ -122,7 +122,7 @@ int gmx_saltbr(int argc,char *argv[])
   const char *desc[] = {
     "[TT]g_saltbr[tt] plots the distance between all combination of charged groups",
     "as a function of time. The groups are combined in different ways.",
-    "A minimum distance can be given, (eg. the cut-off), then groups",
+    "A minimum distance can be given, (ie. a cut-off), then groups",
     "that are never closer than that distance will not be plotted.[BR]",
     "Output will be in a number of fixed filenames, [TT]min-min.xvg[tt], [TT]plus-min.xvg[tt]",
     "and [TT]plus-plus.xvg[tt], or files for every individual ion-pair if the [TT]-sep[tt]",
-- 
2.22.0