Made g_tune_pme work correctly when ir->init_step > 0

For .tpr files with ir->init_step > 0, the benchmarks do not have the
correct number of steps. This fix sets init_step to zero for the benchmark .tpr
files but keeps the original init_step value for the launch .tpr file.
Benchmarking should now work correctly for .tpr files any init_step value,
regardless whether the .cpt file was provided to g_tune_pme or not.

Change-Id: I9d44647d4c71e1514709ee4d6477bd416f455f42
Fix g_msd -mol

Fixes #774

Change-Id: I6fa564754bcbc898a5da6428729775c669cd72d2
Removes unused files

These files are never compiled

Change-Id: I5ccb808b4021b3c081b947ff3a559bb798babbed
SSE2 single-precision kernels

New single-precision x86 kernels rewritten to use intrinsics
instead of raw assembly. SSE2 is now our lowest-supported
accelerated instruction set on x86. We generate kernels for
the same interaction choices as the plain c kernels, but
have not enabled Buckingham interactions SSE kernels since
that would generate a whole lot more kernels that would only
be use in rare circumstances. The neighborsearching routine
has also been updated to optionally generate lists that
are padded up to the simd width, which is set by each
kernel when we initialize the neighborlist.

Change-Id: Ic51078e10e7f1f29af3d33e256177806ec208646
Merge "Removes unused files" into release-4-6
Remove rest of the xml support

* xml_io was removed in bfab7b6030da6cec449429454e2fa9a720474838

Change-Id: If78d923f292cd5f547d88dfa07c42ec31a797c82
Removing Zn and Ar non-OPLS atom types

Some parameters were clearly wrong and the source of them was
not documented. They can be added back in but then the source
needs to be documented.

Add source for Fe2+.

Leaving Cu2+, Fe2+ and SI given their source is documented.

Fixes #957

Change-Id: I82a5b7ae4a54ab2aeb5690cea6256146a9819250
Added grompp warning

Don't silently allow the user to combine velocity generation and an
unconstrained start.

Change-Id: I62f9f917fe583dfccdddfb5f9fad82a17e15ca25
Merge "Removing Zn and Ar non-OPLS atom types" into release-4-6
Merge "Remove rest of the xml support" into release-4-6
Merge "Added grompp warning" into release-4-6
Remove double declaration in headers

Change-Id: Ibaaee5b8bb8c6b3f4cf12c34efd2229f346a838f
Rename remaining GMX_ACCELERATION to GMX_CPU_ACCELERATION

366c49a438150 renamed this variable but forgot these three.

Change-Id: Iad653e2deaa2fc7cb218bffab84c6833ff8b3d56
Fix bugs in gmxCFlags

The first argument to GMX_TEST_CFLAG needs to be unique, otherwise the
test is skipped and the respective options never gets added.

Change-Id: Iaf6f30511735b5b9459520ca72ed5eda6b3b5ec5
Fix GMX_TEST_CFLAG bug with acceleration flags

If a cmake error occured (e.g. fftw not found) between a flag being
tested (e.g. -msse4.1) and the flags being set, then those flags
weren't set. Neither on the first run with the error, nor later
because in later runs GROMACS_C_FLAGS_SET would already be set.

Fixes #1037

Change-Id: Ibc555d885bab5bec04a1aa5b10f06351e6aa6f38
always mark as advanced leftover FindCUDA variables

If the user turned off GMX_GPU after a failed configure pass, some
variables were still left behind. Now these variables are marked as
advanced unconditionally.

Change-Id: Ia20ad5a164b6a8b43801ad1d83bc03332da5f6c1
Merge "Remove double declaration in headers" into release-4-6
SSE4.1 single-precision kernels

Kernels using SSE4.1 instructions on modern Intel and AMD x86 CPUs.
These are not a whole lot faster than SSE2 right now in default
interactions, but for generalized born they probably are due to
better selection instructions. Padding and other properties are
similar to the SSE2 kernels just commited.

Change-Id: I3d6c09c70d16006128320ca24079f7f3851a882e
Add CMAKE_PREFIX_PATH to cmake-gui

CMAKE_PREFIX_PATH didn't show up in ccmake, because it wasn't in
the cache by default. Given that it is the easiest way to specify
external dependendencies it should show up. Also prior one had to go
to the advanced settings to specify the path to FFTW. Modified
the FFTW message to explain that CMAKE_PREFIX_PATH is also an
option. This makes it possible to set it (if it isn't found
automatically)without having to open the advanced settings.

Change-Id: Ib36ab004aac8f65d2a145d67b72b8c8f4fa065c8
Minor updates to CMake usage

Change-Id: Ie917ccd041c7576afb82ddef7b82598f462c7548