Various minor spelling fixes - messages and code comments only.

Subsequent revision: Also update copyright years as necessary.

Change-Id: I04ad9fd4948ea6c8598262cdd4b1fb87e5348248

diff --git a/src/contrib/mkice.c b/src/contrib/mkice.c
index 983900324f4089d796d79c283f567bbd33b1b0bd..51e64e70d367af350fb9a96ec23de941a54bddfa 100644 (file)
--- a/src/contrib/mkice.c
+++ b/src/contrib/mkice.c
@@ -493,7 +493,7 @@ int main(int argc,char *argv[])
     "If an input file is given it is interpreted as a series of oxygen",
     "coordinates the distance between which can be scaled by the odist flag.",
     "The program then adds hydrogens to the oxygens in random orientation",
-    "but with proper OH distances and HOH angle. This feature allows to",
+    "but with proper OH distances and HOH angle. This feature allows one to",
     "build water clusters based on oxygen coordinates only."
   };
   static int nx=1,ny=1,nz=1;

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index e96e408cc3e003a072866ddf2dcd024ac8b62836..84017c079328ee46cdb74c7c78b1e68075c9e3e1 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -9109,7 +9109,7 @@ void dd_partition_system(FILE                *fplog,
          * Box scaling happens at the end of the MD step,
          * after the DD partitioning.
          * We therefore have to do DLB in the first partitioning
-         * after an MD step where P-coupling occured.
+         * after an MD step where P-coupling occurred.
          * We need to determine the last step in which p-coupling occurred.
          * MRS -- need to validate this for vv?
          */

diff --git a/src/gromacs/gmxana/dlist.cpp b/src/gromacs/gmxana/dlist.cpp
index 113df763d43b2e3b5a9236e3e740fd948caa23eb..d065c4ce2d5aee27a465cd4bcabdd13291a770cc 100644 (file)
--- a/src/gromacs/gmxana/dlist.cpp
+++ b/src/gromacs/gmxana/dlist.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
@@ -328,7 +328,7 @@ gmx_bool has_dihedral(int Dih, t_dlist *dl)
             break;
         default:
             pr_dlist(stdout, 1, dl, 1, 0, TRUE, TRUE, TRUE, TRUE, MAXCHI);
-            gmx_fatal(FARGS, "Non existant dihedral %d in file %s, line %d",
+            gmx_fatal(FARGS, "Non existent dihedral %d in file %s, line %d",
                       Dih, __FILE__, __LINE__);
     }
     return b;

diff --git a/src/gromacs/gmxana/gmx_dyndom.cpp b/src/gromacs/gmxana/gmx_dyndom.cpp
index 913d3aa03229e4d843faebee47d957c5f4cdc6ca..d8d8b3a5d6b1c3a11caa7412ac940e0a6c7c0584 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyndom.cpp
+++ b/src/gromacs/gmxana/gmx_dyndom.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
@@ -229,7 +229,7 @@ int gmx_dyndom(int argc, char *argv[])
 
     printf("Select group to rotate:\n");
     rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
-    printf("Going to rotate %s containg %d atoms\n", grpname, isize);
+    printf("Going to rotate %s containing %d atoms\n", grpname, isize);
 
     snew(index_all, atoms.nr);
     for (i = 0; (i < atoms.nr); i++)

diff --git a/src/gromacs/gmxana/gmx_make_edi.cpp b/src/gromacs/gmxana/gmx_make_edi.cpp
index bbbd6f42f8479719921fa62403028da14a03d63e..631d8a0cbaad8bb73424ad09bac3a6ac72342af9 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_edi.cpp
+++ b/src/gromacs/gmxana/gmx_make_edi.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, 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.
@@ -685,7 +685,7 @@ int gmx_make_edi(int argc, char *argv[])
         { "-flood",  FALSE, etSTR, {&evSelections[2]},
           "Indices of eigenvectors for flooding"},
         { "-outfrq", FALSE, etINT, {&edi_params.outfrq},
-          "Freqency (in steps) of writing output in [REF].xvg[ref] file" },
+          "Frequency (in steps) of writing output in [REF].xvg[ref] file" },
         { "-slope", FALSE, etREAL, { &edi_params.slope},
           "Minimal slope in acceptance radius expansion"},
         { "-linstep", FALSE, etSTR, {&evParams[0]},

diff --git a/src/gromacs/gmxana/gmx_rms.cpp b/src/gromacs/gmxana/gmx_rms.cpp
index 80b637ba70c5e5acfa4f9351faa6b8eeff59240d..f51f3ccca450a022be6e4b5dc8f35e56f6e466a3 100644 (file)
--- a/src/gromacs/gmxana/gmx_rms.cpp
+++ b/src/gromacs/gmxana/gmx_rms.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
@@ -134,7 +134,7 @@ int gmx_rms(int argc, char *argv[])
         "otherwise the masses will be deduced from the [TT]atommass.dat[tt] file in",
         "[TT]GMXLIB[tt]. This is fine for proteins, but not",
         "necessarily for other molecules. A default mass of 12.011 amu (carbon)",
-        "is assigned to unknown atoms. You can check whether this happend by",
+        "is assigned to unknown atoms. You can check whether this happened by",
         "turning on the [TT]-debug[tt] flag and inspecting the log file.[PAR]",
 
         "With [TT]-f2[tt], the 'other structures' are taken from a second",

diff --git a/src/gromacs/gmxana/gmx_sans.cpp b/src/gromacs/gmxana/gmx_sans.cpp
index b5df5e4e34b8d449c78a4ed7786673c4b83f1958..b8c523d562ee4a4c7fd7f5e015e82706399ce017 100644 (file)
--- a/src/gromacs/gmxana/gmx_sans.cpp
+++ b/src/gromacs/gmxana/gmx_sans.cpp
@@ -78,7 +78,7 @@ int gmx_sans(int argc, char *argv[])
     };
     static gmx_bool      bPBC     = TRUE;
     static gmx_bool      bNORM    = FALSE;
-    static real          binwidth = 0.2, grid = 0.05; /* bins shouldnt be smaller then smallest bond (~0.1nm) length */
+    static real          binwidth = 0.2, grid = 0.05; /* bins shouldn't be smaller then smallest bond (~0.1nm) length */
     static real          start_q  = 0.0, end_q = 2.0, q_step = 0.01;
     static real          mcover   = -1;
     static unsigned int  seed     = 0;

diff --git a/src/gromacs/gmxana/gmx_sorient.cpp b/src/gromacs/gmxana/gmx_sorient.cpp
index 0040885bb263387c2c23a3f034ccd3f64a216934..968b57d2cde4de6b40218c59fb4acf97e646653a 100644 (file)
--- a/src/gromacs/gmxana/gmx_sorient.cpp
+++ b/src/gromacs/gmxana/gmx_sorient.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
@@ -162,7 +162,7 @@ int gmx_sorient(int argc, char *argv[])
         "consist of 3 atoms per solvent molecule.",
         "Only solvent molecules between [TT]-rmin[tt] and [TT]-rmax[tt] are",
         "considered for [TT]-o[tt] and [TT]-no[tt] each frame.[PAR]",
-        "[TT]-o[tt]: distribtion of [MATH][COS][GRK]theta[grk][SUB]1[sub][cos][math] for rmin<=r<=rmax.[PAR]",
+        "[TT]-o[tt]: distribution of [MATH][COS][GRK]theta[grk][SUB]1[sub][cos][math] for rmin<=r<=rmax.[PAR]",
         "[TT]-no[tt]: distribution of [MATH][COS][GRK]theta[grk][SUB]2[sub][cos][math] for rmin<=r<=rmax.[PAR]",
         "[TT]-ro[tt]: [MATH][CHEVRON][COS][GRK]theta[grk][SUB]1[sub][cos][chevron][math] and [MATH][CHEVRON]3[COS]^2[GRK]theta[grk][SUB]2[sub][cos]-1[chevron][math] as a function of the",
         "distance.[PAR]",
@@ -176,7 +176,7 @@ int gmx_sorient(int argc, char *argv[])
     static real       rmin = 0.0, rmax = 0.5, binwidth = 0.02, rbinw = 0.02;
     t_pargs           pa[] = {
         { "-com",  FALSE, etBOOL,  {&bCom},
-          "Use the center of mass as the reference postion" },
+          "Use the center of mass as the reference position" },
         { "-v23",  FALSE, etBOOL,  {&bVec23},
           "Use the vector between atoms 2 and 3" },
         { "-rmin",  FALSE, etREAL, {&rmin}, "Minimum distance (nm)" },

diff --git a/src/gromacs/gmxana/gmx_spol.cpp b/src/gromacs/gmxana/gmx_spol.cpp
index a9a4389f04b848d32b3ad71f14f769ccb83182d8..571284b1ee5314b6a4ddbf76cc8f32cecd34550d 100644 (file)
--- a/src/gromacs/gmxana/gmx_spol.cpp
+++ b/src/gromacs/gmxana/gmx_spol.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
@@ -198,7 +198,7 @@ int gmx_spol(int argc, char *argv[])
     static real       rmin   = 0.0, rmax = 0.32, refdip = 0, bw = 0.01;
     t_pargs           pa[]   = {
         { "-com",  FALSE, etBOOL,  {&bCom},
-          "Use the center of mass as the reference postion" },
+          "Use the center of mass as the reference position" },
         { "-refat",  FALSE, etINT, {&srefat},
           "The reference atom of the solvent molecule" },
         { "-rmin",  FALSE, etREAL, {&rmin}, "Maximum distance (nm)" },

diff --git a/src/gromacs/gmxana/gmx_tune_pme.cpp b/src/gromacs/gmxana/gmx_tune_pme.cpp
index eaf69856ba4e3ba12cbd088073ed81f8b2556ba0..adf950b8356c4e50042516cc88dff41fe8c391e6 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.cpp
+++ b/src/gromacs/gmxana/gmx_tune_pme.cpp
@@ -273,7 +273,7 @@ static int parse_logfile(const char *logfile, const char *errfile,
                     }
                     iFound = eFoundDDStr;
                 }
-                /* Catch a few errors that might have occured: */
+                /* Catch a few errors that might have occurred: */
                 else if (str_starts(line, "There is no domain decomposition for"))
                 {
                     fclose(fp);
@@ -362,7 +362,7 @@ static int parse_logfile(const char *logfile, const char *errfile,
             {
                 if (fgets(line, STRLEN, fp) != NULL)
                 {
-                    fprintf(stderr, "\nWARNING: An error occured during this benchmark:\n"
+                    fprintf(stderr, "\nWARNING: An error occurred during this benchmark:\n"
                             "%s\n", line);
                 }
                 fclose(fp);
@@ -1471,7 +1471,7 @@ static void do_the_tests(
         "Number of PP ranks has a prime factor that is too large.",
         "The number of PP ranks did not suit the number of GPUs.",
         "Some GPUs were not detected or are incompatible.",
-        "An error occured."
+        "An error occurred."
     };
     char        str_PME_f_load[13];
 

diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
index 0fd8b7774001d8c308cd7c688b4ca39e900900f8..63d2730a3767f91e784f951d631d1b6dc4c48761 100644 (file)
--- a/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@ -2454,7 +2454,7 @@ void read_pull_xf(const char *fn, const char *fntpr, t_UmbrellaHeader * header,
                 {
                     if (gUsed >= window->nPull)
                     {
-                        gmx_fatal(FARGS, "gUsed too large (%d, nPull=%d). This error should have been catched before.\n",
+                        gmx_fatal(FARGS, "gUsed too large (%d, nPull=%d). This error should have been caught before.\n",
                                   gUsed, window->nPull);
                     }
 
@@ -3440,7 +3440,7 @@ int gmx_wham(int argc, char *argv[])
         { "-ac-trestart", FALSE, etREAL, {&opt.acTrestart},
           "When computing autocorrelation functions, restart computing every .. (ps)"},
         { "-acred", FALSE, etBOOL, {&opt.bAllowReduceIact},
-          "HIDDENWhen smoothing the ACTs, allow to reduce ACTs. Otherwise, only increase ACTs "
+          "HIDDENWhen smoothing the ACTs, allows one to reduce ACTs. Otherwise, only increase ACTs "
           "during smoothing"},
         { "-nBootstrap", FALSE,  etINT, {&opt.nBootStrap},
           "nr of bootstraps to estimate statistical uncertainty (e.g., 200)" },

diff --git a/src/gromacs/gmxana/nsfactor.cpp b/src/gromacs/gmxana/nsfactor.cpp
index ed45c348c10da5963493b667b418088002d42b58..48551926f7c4f86f6e9c84bb84e38619ed5031de 100644 (file)
--- a/src/gromacs/gmxana/nsfactor.cpp
+++ b/src/gromacs/gmxana/nsfactor.cpp
@@ -58,7 +58,7 @@ void check_binwidth(real binwidth)
     real smallest_bin = 0.1;
     if (binwidth < smallest_bin)
     {
-        gmx_fatal(FARGS, "Binwidth shouldnt be smaller then smallest bond length (H-H bond ~0.1nm) in a box");
+        gmx_fatal(FARGS, "Binwidth shouldn't be smaller then smallest bond length (H-H bond ~0.1nm) in a box");
     }
 }
 

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.cpp b/src/gromacs/gmxpreprocess/gen_vsite.cpp
index 6525bd1aa550d10b5d0c9dac119b5705df266e9e..8c4bed2ee4ad5aee8b3bb900132cafd737977d82 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.cpp
+++ b/src/gromacs/gmxpreprocess/gen_vsite.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
@@ -1196,7 +1196,7 @@ static int gen_vsites_tyr(gpp_atomtype_t atype, rvec *newx[],
      * when we constrain both CG-HH and OH-HH distances. Instead of requiring
      * the use of lincs_order=8 we introduce a dummy mass three times further
      * away from OH than HH. The mass is accordingly a third, with the remaining
-     * 2/3 moved to OH. This shouldnt cause any problems since the forces will
+     * 2/3 moved to OH. This shouldn't cause any problems since the forces will
      * apply to the HH constructed atom and not directly on the virtual mass.
      */
 

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index 038b3d067bb0b8fe3865925e3a91858695139292..c06ce7836ed981202aa7caabb39e8f1a8618dfbd 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -616,10 +616,10 @@ void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
                 (int)fep->sc_r_power);
         CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
 
-        sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
+        sprintf(err_buf, "Can't use positive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
         CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) ||  (fep->init_lambda > 0)));
 
-        sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
+        sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
         CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
 
         sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
@@ -4065,7 +4065,7 @@ void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
         {
             sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
             CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
-            sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
+            sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
                     i, ir->opts.tau_t[i]);
             CHECK(ir->opts.tau_t[i] < 0);
         }

diff --git a/src/gromacs/math/utilities.h b/src/gromacs/math/utilities.h
index 768653169e2ec4b116d55f610d03e13e02c0a071..d0885651b162a311e4f25991762952edc22d2102 100644 (file)
--- a/src/gromacs/math/utilities.h
+++ b/src/gromacs/math/utilities.h
@@ -121,7 +121,7 @@ gmx_numzero(double a);
 
 /*! \brief Multiply two large ints
  *
- * \return False iff overflow occured
+ * \return False iff overflow occurred
  */
 gmx_bool
 check_int_multiply_for_overflow(gmx_int64_t  a,

diff --git a/src/gromacs/mdlib/clincs.cpp b/src/gromacs/mdlib/clincs.cpp
index 9fcbf8c696fc096deab2b6355656eda5f03fcfc6..f5224bbebbb74a71551aeff2a97a19acfe7efd1e 100644 (file)
--- a/src/gromacs/mdlib/clincs.cpp
+++ b/src/gromacs/mdlib/clincs.cpp
@@ -2415,7 +2415,7 @@ gmx_bool constrain_lincs(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
 
         /* This bWarn var can be updated by multiple threads
          * at the same time. But as we only need to detect
-         * if a warning occured or not, this is not an issue.
+         * if a warning occurred or not, this is not an issue.
          */
         bWarn = FALSE;
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre
index 5af77c5ce97539c9d307e68bfe699f8cd9387c4b..7c412dc02855bbc041223d56e0c6b9efa10e1bc8 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, 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.
@@ -205,7 +205,7 @@ void
     {{
         if (ic->ljpme_comb_rule == eljpmeLB)
         {{
-            gmx_incons("The nbnxn SIMD kernels don't suport LJ-PME with LB");
+            gmx_incons("The nbnxn SIMD kernels don't support LJ-PME with LB");
         }}
         vdwkt = vdwktLJEWALDCOMBGEOM;
     }}

diff --git a/src/gromacs/pbcutil/mshift.cpp b/src/gromacs/pbcutil/mshift.cpp
index 92bbdd7b7ae480c0fcc160cf5264088662ac4245..404a9d83cd14db25f0f18542d71c778f3c9f0264 100644 (file)
--- a/src/gromacs/pbcutil/mshift.cpp
+++ b/src/gromacs/pbcutil/mshift.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
@@ -147,7 +147,7 @@ static void mk_igraph(t_graph *g, int ftype, const t_ilist *il,
 
 gmx_noreturn static void g_error(int line, const char *file)
 {
-    gmx_fatal(FARGS, "Tring to print non existant graph (file %s, line %d)",
+    gmx_fatal(FARGS, "Trying to print nonexistent graph (file %s, line %d)",
               file, line);
 }
 #define GCHECK(g) if (g == NULL) g_error(__LINE__, __FILE__)

diff --git a/src/gromacs/trajectoryanalysis/modules/rdf.cpp b/src/gromacs/trajectoryanalysis/modules/rdf.cpp
index a808ebb9084a5027ad5a65125752708b99db136b..958a67b9c6cb071946a4882bf46400af88e29aeb 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/rdf.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/rdf.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
@@ -225,7 +225,7 @@ Rdf::initOptions(IOptionsContainer *options, TrajectoryAnalysisSettings *setting
 {
     const char *const desc[] = {
         "[THISMODULE] calculates radial distribution functions from one",
-        "refernce set of position (set with [TT]-ref[tt]) to one or more",
+        "reference set of position (set with [TT]-ref[tt]) to one or more",
         "sets of positions (set with [TT]-sel[tt]).  To compute the RDF with",
         "respect to the closest position in a set in [TT]-ref[tt] instead, use",
         "[TT]-surf[tt]: if set, then [TT]-ref[tt] is partitioned into sets",

diff --git a/src/gromacs/trajectoryanalysis/modules/sasa.cpp b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
index 1e30e4ff5184df5e3baab4ef83b73fa4ff49b2fe..bd440203e22708e8e4a20cd833bab1ae9150305d 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/sasa.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
@@ -185,7 +185,7 @@ void do_conect(const char *fn, int n, rvec x[])
     {
         if ((c[i].aa == -1) || (c[i].ab == -1))
         {
-            fprintf(stderr, "Warning dot %d has no conections\n", i+1);
+            fprintf(stderr, "Warning dot %d has no connections\n", i+1);
         }
         fprintf(fp, "CONECT%5d%5d%5d\n", i+1, c[i].aa+1, c[i].ab+1);
     }

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index 0eb49bf1b6dfc0b452493fa05992c85c66f85467..641f513278676d694c77e54258f09f86bb7ff126 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -214,8 +214,8 @@ int gmx_mdrun(int argc, char *argv[])
         "the [TT]mdrun[tt] process that is the parent of the others.",
         "[PAR]",
         "Interactive molecular dynamics (IMD) can be activated by using at least one",
-        "of the three IMD switches: The [TT]-imdterm[tt] switch allows to terminate the",
-        "simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
+        "of the three IMD switches: The [TT]-imdterm[tt] switch allows one to terminate",
+        "the simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
         "[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
         "IMD remote can be turned on by [TT]-imdpull[tt].",
         "The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",