Set return value to FALSE (0) in estimate_dt in libxdrf.c

To be on the safe side the function to estimate the time
step betwen frames was fixed such that the return value
bOK is always set even if the file was missing or empty.
In addition the function is made static since it is not
used outside the file.

Change-Id: I8706a23b7a198f9d0718f1bfcb4a7770b2e6e53c
Removed obsolete hint in error message.

GMX_RESET_COUNTER was removed from the code a long time ago.

Change-Id: I2fb54995f1a6e211995ef0474bcdb36f5018550d
Fixed Pulp Fiction quote

Fixes 1011

Change-Id: I40bfdca8906505a8a619c6ba2db924a50b830af5
Fix large file support

Variables containing flags need to be cached. Before config.h
was written correct on first run but rerunning cmake caused
flags to be ommited. Also fixed test program.

Change-Id: Id948c54766547a85ac84751762de3afba21ea576
Fixed Bug #593 about memory hole in trjcat.

Fixed by explicitly freeing memory for each frame. Tested to make
sure it does not crash.

Change-Id: Ic0e91b828a1e5a23f38690b4753092a31e6c4db4
fix CUDA non-bonded kernel pointer assignment

The plain cut-off kernel pointer was incorrectly set which caused kernel
launch error.

Change-Id: Id4d71c4e04e8775134ee95e5ebb8c79cda7e8bf8
enable GMX_PREFER_STATIC_LIBS CMake option on Mac OS X

Change-Id: Ifa01573e514bc1a167095023e26c77829eda7b42
fix false positive gcc 4.7 warning in libxdrf

Change-Id: Ied3b07dca011ca142455c328cba25b0b01eadb8c
Merge "fix CUDA non-bonded kernel pointer assignment" into release-4-6
fixed incorrect group energies with nbnxn CPU kernels

Fixed two energy group indexing errors in the nbnxn CPU kernels.
The code has now been generalized and we avoid code duplication.

Change-Id: I524d0d2c86b54a92ae124f2c067ccef3daac1515
set the default for nstdhdl to 100

The default for nstdhdl was 10, which was not a multiple of the default
for nstcalcenergy (100). This caused a warning in grompp. Also 100 should
still result in correlated samples.
Removed nstfep from mdp_opt.html.

Change-Id: If9969f27b9dafb71a7c4a81b929ff3f9455f4cf8
Merge "set the default for nstdhdl to 100" into release-4-6
fixed incorrect PME load balancing limitation

PME load balancing would not work with -dlb=auto but DD-DLB not active (yet).
Also fixed incorrect cut-off in PME DLB limited message.

Change-Id: I717981743403de36c747108e0c3e907d6213be10
Merge "Fixed Pulp Fiction quote" into release-4-5-patches
Merge "fix false positive gcc 4.7 warning in libxdrf" into release-4-6
Merge "enable GMX_PREFER_STATIC_LIBS CMake option on Mac OS X" into release-4-6
Merge "fixed incorrect PME load balancing limitation" into release-4-6
Fix usage of CMAKE_REQUIRED_*

Always reset all variables.
Only require libm if it is avaiable (only on Unix)

Also prefer usage of _finite. ICC on Windows gives warnings
for isfinite (we don't inlude mathimf.h).

Fixes #998

Change-Id: Ib7c064aaf6d26d2ab96f5e88345091a2eb096998
Merge "Fix large file support" into release-4-5-patches
Set HAVE_FSEEKO consistently in one place

HAVE_FSEEKO was set in two places and the definition wasn't
consistent. Now only the one in gmxTestLargeFiles is used.
HAVE_FSEEKO is only used if it fully works and 64bit fseek is
available.

Change-Id: I5c8f837e414f1ddeab0de8148d5a9c91047116f8