Force g_bond to use structure file

Previous versions of Gromacs never wrote broken molecules, but
this is no longer true for domain decomposition. Box dimensions
are set from the trajectory, but the molecular connectivity
from the structure file.

Fixes #834.

Change-Id: I61ecb4957ef11e03bfeef10095a406cbddd23a34

diff --git a/src/tools/gmx_bond.c b/src/tools/gmx_bond.c
index ee2894932f03eefe3a242e7e5aca982aee17b2f1..566e161bb86bd3bd0f7ae35a17ca43e80c2fdb6c 100644 (file)
--- a/src/tools/gmx_bond.c
+++ b/src/tools/gmx_bond.c
@@ -276,7 +276,8 @@ static void do_bonds(FILE *log, const char *fn, const char *fbond,
 int gmx_bond(int argc, char *argv[])
 {
     const char     *desc[] = {
-        "[TT]g_bond[tt] makes a distribution of bond lengths. If all is well a",
+        "[TT]g_bond[tt] makes a distribution of bond lengths by using the",
+        "connectivity information in the structure file. If all is well a",
         "Gaussian distribution should be made when using a harmonic potential.",
         "Bonds are read from a single group in the index file in order i1-j1",
         "i2-j2 through in-jn.[PAR]",
@@ -284,12 +285,11 @@ int gmx_bond(int argc, char *argv[])
         "of the bondlength ([TT]-blen[tt]). That means, for a bond of 0.2",
         "a tol of 0.1 gives a distribution from 0.18 to 0.22.[PAR]",
         "Option [TT]-d[tt] plots all the distances as a function of time.",
-        "This requires a structure file for the atom and residue names in",
-        "the output. If however the option [TT]-averdist[tt] is given (as well",
+        "If however the option [TT]-averdist[tt] is given (as well",
         "or separately) the average bond length is plotted instead."
     };
     const char     *bugs[] = {
-        "It should be possible to get bond information from the topology."
+        "It should be possible to get information about specific bonds from the topology."
     };
     static real     blen  = -1.0, tol = 0.1;
     static gmx_bool bAver = TRUE, bAverDist = TRUE;
@@ -318,7 +318,7 @@ int gmx_bond(int argc, char *argv[])
     t_filenm        fnm[] = {
         { efTRX, "-f", NULL, ffREAD  },
         { efNDX, NULL, NULL, ffREAD  },
-        { efTPS, NULL, NULL, ffOPTRD },
+        { efTPS, NULL, NULL, ffREAD },
         { efXVG, "-o", "bonds", ffWRITE },
         { efLOG, NULL, "bonds", ffOPTWR },
         { efXVG, "-d", "distance", ffOPTWR }
@@ -330,6 +330,8 @@ int gmx_bond(int argc, char *argv[])
                       NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
                       &oenv);
 
+    read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, FALSE);
+
     if (bAverDist)
     {
         fdist = opt2fn("-d", NFILE, fnm);
@@ -337,11 +339,6 @@ int gmx_bond(int argc, char *argv[])
     else
     {
         fdist = opt2fn_null("-d", NFILE, fnm);
-        if (fdist)
-        {
-            read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box,
-                          FALSE);
-        }
     }
 
     rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);