Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches

diff --git a/src/kernel/runner.c b/src/kernel/runner.c
index a3a8fdea51094c3fea3a154d0e86d8bfc5a0b131..888fe31b7435a760707686e15abc155c356c040d 100644 (file)
--- a/src/kernel/runner.c
+++ b/src/kernel/runner.c
@@ -446,6 +446,12 @@ int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
             );
     }
 
+    if ((Flags & MD_RERUN) &&
+        (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
+    {
+        gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
+    }
+
     if (can_use_allvsall(inputrec,mtop,TRUE,cr,fplog))
     {
         /* All-vs-all loops do not work with domain decomposition */

diff --git a/src/tools/gmx_sas.c b/src/tools/gmx_sas.c
index 573e3968a12c93d186a2196b079dec00e5803b48..cb6ac71c58a6d2ee33abef77376a2b78ba6a2ef3 100644 (file)
--- a/src/tools/gmx_sas.c
+++ b/src/tools/gmx_sas.c
@@ -226,6 +226,7 @@ void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
   const char   *flegend[] = { "Hydrophobic", "Hydrophilic", 
                              "Total", "D Gsolv" };
   const char   *vlegend[] = { "Volume (nm\\S3\\N)", "Density (g/l)" };
+  const char   *or_and_oa_legend[] = { "Average (nm\\S2\\N)", "Standard deviation (nm\\S2\\N)" };
   const char   *vfile;
   real         t;
   gmx_atomprop_t aps=NULL;
@@ -499,10 +500,12 @@ void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
       atom_area2[i] /= nfr;
     }
     fprintf(stderr,"Printing out areas per atom\n");
-    fp  = xvgropen(opt2fn("-or",nfile,fnm),"Area per residue","Residue",
+    fp  = xvgropen(opt2fn("-or",nfile,fnm),"Area per residue over the trajectory","Residue",
                   "Area (nm\\S2\\N)",oenv);
-    fp2 = xvgropen(opt2fn("-oa",nfile,fnm),"Area per atom","Atom #",
+    xvgr_legend(fp, asize(or_and_oa_legend),or_and_oa_legend,oenv);
+    fp2 = xvgropen(opt2fn("-oa",nfile,fnm),"Area per atom over the trajectory","Atom #",
                   "Area (nm\\S2\\N)",oenv);
+    xvgr_legend(fp2, asize(or_and_oa_legend),or_and_oa_legend,oenv);
     if (bITP) {
       fp3 = ftp2FILE(efITP,nfile,fnm,"w");
       fprintf(fp3,"[ position_restraints ]\n"
@@ -570,7 +573,7 @@ int gmx_sas(int argc,char *argv[])
     "and a group for the output. The calculation group should always",
     "consists of all the non-solvent atoms in the system.",
     "The output group can be the whole or part of the calculation group.",
-    "The area can be plotted",
+    "The average and standard deviation of the area over the trajectory can be plotted",
     "per residue and atom as well (options [TT]-or[tt] and [TT]-oa[tt]).",
     "In combination with the latter option an [TT]itp[tt] file can be",
     "generated (option [TT]-i[tt])",