Merge branch release-5-1 into release-2016

Change-Id: I976ad584d1c8757c6464aae482cb5a4c245beacb

diff --git a/docs/user-guide/environment-variables.rst b/docs/user-guide/environment-variables.rst
index 04fc25ba13e96f8d7d626ffeba7cd0a51c6aa688..9b4114081bc3df82af669e9d3ac37df2080f40b4 100644 (file)
--- a/docs/user-guide/environment-variables.rst
+++ b/docs/user-guide/environment-variables.rst
@@ -181,6 +181,10 @@ Performance and Run Control
         when set, disables GPU detection even if :ref:`gmx mdrun` was compiled
         with GPU support.
 
+``GMX_GPU_APPLICATION_CLOCKS``
+        setting this variable to a value of "0", "ON", or "DISABLE" (case insensitive)
+        allows disabling the CUDA GPU allication clock support.
+
 ``GMX_DISRE_ENSEMBLE_SIZE``
         the number of systems for distance restraint ensemble
         averaging. Takes an integer value.

diff --git a/src/gromacs/gmxana/gmx_dos.cpp b/src/gromacs/gmxana/gmx_dos.cpp
index 9737716eb88465830b0f8e34e93d70c6e3589859..88a3667a365e329fa6ad3854fef321f92686f3f9 100644 (file)
--- a/src/gromacs/gmxana/gmx_dos.cpp
+++ b/src/gromacs/gmxana/gmx_dos.cpp
@@ -286,9 +286,10 @@ int gmx_dos(int argc, char *argv[])
     double              invNormalize;
     gmx_bool            normalizeAutocorrelation;
 
-    static     gmx_bool bVerbose = TRUE, bAbsolute = FALSE, bNormalizeDos = FALSE;
-    static     gmx_bool bRecip   = FALSE;
-    static     real     Temp     = 298.15, toler = 1e-6;
+    static     gmx_bool bVerbose   = TRUE, bAbsolute = FALSE, bNormalizeDos = FALSE;
+    static     gmx_bool bRecip     = FALSE;
+    static     real     Temp       = 298.15, toler = 1e-6;
+    int                 min_frames = 100;
 
     t_pargs             pa[]     = {
         { "-v", FALSE, etBOOL, {&bVerbose},
@@ -398,6 +399,10 @@ int gmx_dos(int argc, char *argv[])
 
     close_trj(status);
 
+    if (nframes < min_frames)
+    {
+        gmx_fatal(FARGS, "You need at least %d frames in the trajectory and you only have %d.", min_frames, nframes);
+    }
     dt = (t1-t0)/(nframes-1);
     if (nV > 0)
     {