added missing cleanup of some nbnxn_cuda data

While the content of the data structures the pointers in nbnxn_cuda
point to was freed up, the data structures themselves were not.

Change-Id: Icb1c5da9867ee252e2a6dadf7f164d7bb4f41a26
Set version info for 4.6.x release series

Change-Id: I31378a7ef5d9b7333aa91f076c2a792072d304f9
Re-licenced FindGROMACS.cmake (was written by me)

Change-Id: If6a94c561933cbc6db9d47d5a364f75e7fdf5e13
Merge "Set version info for 4.6.x release series" into release-4-6
Moved a few comments back into position

No code changes whatsoever - just formatted some multi-line comments
which uncrustify could not understand.

Change-Id: I85e2f58681c61be937315414dc2a708974b027f8
Updated html manual to 4.6

Change-Id: I2d66c41c56a44fddc31bba823a264795c07d078a
Fix TOUPPER usage

The last argument is the variable name, thus it shouldn't be ${..}.
Caused compile error when setting accleration to sse2, because
TOUPPER wasn't done correctly.

Change-Id: I0087a6cf3c9a160862757f561b5782c0ac253df8
Merge "added missing cleanup of some nbnxn_cuda data" into release-4-6
Merge "Updated html manual to 4.6" into release-4-6
Merge "Fix TOUPPER usage" into release-4-6
Illegal acceleration defaulted to QPX

Change-Id: I1bfd9c7bc7bac68944fd912bda84e8bd03af1fbc
Merge "Re-licenced FindGROMACS.cmake (was written by me)" into release-4-6
Merge "Illegal acceleration defaulted to QPX" into release-4-6
added back cuda.h includes to fix missing CUDA_VERSION

nvcc doesn't define its version identity macro, CUDA_VERSION, by default,
but this needs to be pulled in through cuda.h. Quite weird and
non-standard behavior, but as swithing to legacy kernels and certain
kernel optimizations are broken now, to fix these we need to include
cuda.h.

Change-Id: I4836335e97a287e18e595c160819db2e46a8d798
Merge "Moved a few comments back into position" into release-4-6
fixed copyright of adress kernel

Change-Id: I21816431b4f77210a93dedc7a265c10f074502c4
AdResS: fixes bug in the neighbour list routine

* coarse-grained interactions were not excluded in the all-atom region
* Some atomistic interactions were not excluded in the coarse-grained region

Change-Id: Ib4ac145722367cf139ad3d23b86f0de1ca9d6caf
PME-only counters are now reset with -maxh -resethway

Fixes #1125
For clarity gmx_pme_recv_q_x now returns and enum
and gmx_pme_send_switch is renamed to gmx_pme_send_switchgrid.

Change-Id: I21952780f0b719378d947a79324c844ccde7160a
cmake: fixed typo in template CMakeLists.txt

* prevented build after make clean, when build was used before

Change-Id: I0ba88b36752801c3d492d46c71327fb966edb508
Fixed flop counting for generic cg/adress kernels

Change-Id: I95f2a68a0de64f479820143fdba09ea09805fa93