Merge release-5-0 into release-5-1

Conflicts:
    src/gromacs/gmxpreprocess/grompp.c (adjacent changes, took both)

Additionally, added a declaration for a variable in sasa.cpp that had
been removed from enclosing scopes.

Change-Id: I15c10ef00416aa1f791a58b97d79669efab9a1c5

diff --cc src/gromacs/gmxpreprocess/grompp.c
index 77bb8515f94b3122cdc720da099644b0b9060bf1,0983650920dc88dc5cccafcd9ef21d8910183fa8..2f976b8d2eef1c8667d524a3ac287ca999f9aef2
--- 1/src/gromacs/gmxpreprocess/grompp.c
--- 2/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@@ -1484,8 -1475,10 +1484,10 @@@ int gmx_grompp(int argc, char *argv[]
          "You then supply the old checkpoint file directly to [gmx-mdrun]",
          "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
          "like output frequency, then supplying the checkpoint file to",
 -        "[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
 +        "[THISMODULE] with [TT]-t[tt] along with a new [REF].mdp[ref] file",
-         "with [TT]-f[tt] is the recommended procedure.[PAR]",
+         "with [TT]-f[tt] is the recommended procedure. Actually preserving",
+         "the ensemble (if possible) still requires passing the checkpoint",
+         "file to [gmx-mdrun] [TT]-cpi[tt].[PAR]",
  
          "By default, all bonded interactions which have constant energy due to",
          "virtual site constructions will be removed. If this constant energy is",

diff --cc src/gromacs/mdlib/compute_io.c
Simple merge

diff --cc src/gromacs/mdlib/perf_est.c
Simple merge

diff --cc src/gromacs/trajectoryanalysis/modules/sasa.cpp
index 674a5fa265aabb5bbe24e0b3c29a136022ce11ce,24507bf04ec5bbe41018b82486f1af5cc84608ba..cf243b44190d23983da444ea20e2e5edeaa7291d
--- 1/src/gromacs/trajectoryanalysis/modules/sasa.cpp
--- 2/src/gromacs/trajectoryanalysis/modules/sasa.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
@@@ -667,6 -666,8 +667,8 @@@ Sasa::initAnalysis(const TrajectoryAnal
          }
          {
              AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
 -            prevResind  = -1;
 -            int row     = 0;
++            int prevResind = -1;
++            int row        = 0;
              for (int i = 0; i < surfaceSel_.posCount(); ++i)
              {
                  const int atomIndex     = surfaceSel_.position(i).atomIndices()[0];