Merge remote-tracking branch 'gromacs/release-4-6' into release-4-6-TPI_modifications
Merge remote-tracking branch 'gromacs/release-4-6' into release-4-6-TPI_modifications
Fixed return value of gmx_mtop_bondeds_free_energy

The return value was always true, which was harmless, since it 
could only cause a small performance hit of useless sorting.

Fixes #1387

Change-Id: I088a3747ddb3517fbb5e416b791bd542bd49fed2
Version bumps before release

Change-Id: I5b5ea233c47ce95474dae3b0f71a4ae6ae704f6c
Version bump after 4.6.5 release

Change-Id: I1d1c1ee28d585b6cf4431f9f1ec1a334f68ae6e3
Fix non-critical typo in #ifdef GMX_OMPEN_MP

Added #include to make it work.

Change-Id: Icea244c4fb63aee6ae67a29370d08177a66129a8
Fixed compilation issue due to gcc4.8

by turning off warnings.

Change-Id: Ice3dd8dec8cb9dc590fb293c1face3ed603f7abb
Fixed essential dynamics (ED) continuation from .cpt for reference=average

ED runs where the reference and average structure indices are the same can
crash when continued from checkpoint. For these cases (where reference =
average atom indices) obviously the set of atomic positions for the reference
and average structures is always identical. Therefore, only one of the two
structures is stored (which is the average structure edi->sav). When reading
the old values of these structures from the checkpoint file, edi->sav.x_old
therefore needs to be copied both to xstart and xfit in init_edsam().

Change-Id: Ieb1f029f4a927999dfb4579ee7c3bebe15071dc8
Essential dynamics: move bNeedDoEdsam evaluation to separate function

The bool variable edi->bNeedDoEdsam is used to signal whether any essential
dynamics constraints have to be evaluated for the ED group. This variable
was evaluated at the beginning of an ED simulation in write_edo_legend().
The latter is however not called if continuing from checkpoint. To
get rid of having to remember whether edi->bNeedDoEdsam was already
initialized, there is now a function bNeedDoEdsam(edi) that is evaluated
every time when called.
Also corrected a few typos.

Change-Id: Iab899a677a85ee8270354859c98cc9e5a9db34b7
Pass on default value of radstep in make_edi

This is a bugfix for make_edi when -radfix is chosen. Problem was:
if the user did not specify -radstep, then the default value of 0
was not written to the sam.edi output file. Now it is. Also
renamed "radfix" variable to "radstep" because that better reflects
what it is.

Change-Id: I0cc6ee84d42b18ee0ea6b045cdfb0c1d55d51b9f
cmake: make GMX_BUILD_OWN_FFTW work without fortran compiler

Fixes #1412

Change-Id: I4739c112630ad7e264ce314d2da0b29932ea3041
Patch for Native Client builds.

This patch contains the source changes necessary to compile Gromacs
for Native Client.  Patch is based on original work by Ivan Krasin,
additional changes from Joseph Coffland.
Also included are a few compiler warning fixes and a minor FAHCORE
tweak.

Change-Id: I085c52ff1d8e45ec8ffb8c56f5877313d6225bb2
Checkpointing fix for Native Client

Native Client doesn't allow file renames.  We can over-write output
files, however.  For checkpoints, live dangerously and skip backups.
The alternate would be to use an in-memory file system, but then we're
still screwed if the program gets killed partway through writing the
on-disk version.  Other alternates:  keep all checkpoints.

Change-Id: I952ee6436e69f015633a150f94fca65c7271c6bb
Fixed precision in thermal expansion coefficient calc.

Loss of accuracy was caused by different sampling
of volume and enthalpy and as a result alpha was
computed incorrectly. With the present "fix" the volume
and enthalpy are both downsampled to what is written
in the .edr file. The real fix would be to store the product
of H and V in the .edr file, but that falls outside the
4.6 branch policy.

Change-Id: I1be06d689002d7c9d6be92bf1e377912f0be1efd
Merge remote-tracking branch 'gromacs/release-4-6' into release-4-6-TPI_modifications
Merge branch 'release-4-6-TPI_modifications' of github.com:schlaicha/gromacs into release-4-6-TPI_modifications