Added package version to tng_io CMakelists.txt

Without a package version (for tng_io), the CMake 3 beta
versions will issue warnings.

Fixes #1477.

Change-Id: I4a8f64f70e7372118eecfebb69b4a24cd18835cb
Modify single/double EPS to agree with ISO C

The previous Gromacs values were a factor 2 too tight. While
we're at it, we also added float modifiers to the single-precision
constants, increased the accuracy in the double max/min values,
and improved the least significant bit in one of the single-precision
values. The previous relative accuracies for the PME correction
analytical approximations where set fairly arbitrary by dividing a
tightly chose constant with GMX_REAL_EPS, and since this is now a
larger number the unit test tolerance for those corrections has been
increased slightly to avoid triggering false failures.

Fixes #1356.

Change-Id: If29d2ff4141d86fd019e0dbdbfb7737ead28c3d4
Fixed the output format of g_principal

Gromacs-4.6 and earlier versions had the output transposed. This
patch fixes it such that paxisN.dat contains the x/y/z components
of the N:th prinicipal axis. The default file output names have
been changed to paxisN.dat to increase the probability that users
who rely on old scripts will need to read the help text and find
the changed format.

Fixes #1441, related to #609.

Change-Id: Ic1ed9370145d3389ae8f43c2a419765dabf3a66f
Set make_ndx max name length and count to 1024

Limits were 30, which was a bit on the low side.
Fixes #1512

Change-Id: I62d5146fdac06b7b5b7f56925addeca561c83173
Install libraries in correct directories on multiarch systems.

NB: this patch may change the default install dirs on some systems,
and will _not_ overwrite previous installations. Thus make sure to
link to the correct library versions of e.g. libgromacs.

Fixes #591 and #623.

Change-Id: Ibd1d7d216236a0f5841ba9f0ac622a3f8f1a8718
Replaced gmx_hostname_num by gmx_physicalnode_id_hash

gmx_hostname_num was only used to distinguish physical nodes.
Since it only worked for hostnames with numbers, we replaced it
by a hash of the hostname.

Fixes #1513

Change-Id: I8e60757707386f43269afe0bb38e8500decefcd6
Decoupled repl_ex_nst from nstcalcenergy

The replica exchange frequency is automatically changed by mdrun
to a multiple of nstcalcenergy, which is annoying. It turns out that
it doesn't need to be a multiple, so this changing has been removed.
Fixes #1494

Change-Id: I00833f92fd468924f61879aff8b7c85fe79d3c2e
Always write output from genion

To facilitate scripting we now copy the input conformation
and write it to the output, even if no ions are to be added.

Refs #1458.

Change-Id: I3e467169e30bc7448758c2d506ca35f49b001b50
Removed undocumented -map and -mdata options from g_sham.

Both options and code were completely undocumented, and
nobody seemed interested in helping document them for the
last two years, so for now they are gone.

Fixes #812.

Change-Id: I4d60cf3d58da89d76a4461cdc2e75f031676d2c9
Cleanup environment variables.

Renamed variables to more descriptive names and
removed unused ones.

Fixes #976.

Change-Id: I0c17443c93efe581bf728f783893181e5a7f8ed8
Make nbnxn template and generated files match

Change-Id: I80b80e242d920862a64db22ae2321dcdb532faa1
Added tip5pe water model to oplsa.

The model introduces a small modification to the tip5p model
to reproduce better experimental data for simulations using
Ewald summation.

Reference publication J. Chem. Phys. 120 (2004) 6085-6093.

Fixes #1016.

Change-Id: I1afba614d65d1e4e8eb8594e99eea41e31f1e391
Small changes in appendix A of the manual.

Final fixes #552.

Change-Id: I8e7939ae70eb14d2e1fc0a25b50774d472889bd1
Made mdrun warn when generic kernels are used

mdrun now issues a warning if the generic group-scheme, or plain-C
Verlet-scheme kernels actually did some work. Such kernels should not
be called during routine use of mdrun.

It would be possible to do the check for the use of the generic
group-scheme kernel earlier in mdrun, but it's not easy to ensure we
only write the output at the first such step. Given that the group
scheme is deprecated, warning only at the end is sufficiently nice
behaviour.

Change-Id: Ib9b15165e53510f537687a4b448aaa01f1418522
Added reference to cmap in pdb2gmx.

Fixes #886.

Change-Id: Ib4c84a50962ed90ce145ad001322a9a46c8a2ab0
Merge release-5-0 into master

Conflicts:
- src/gromacs/legacyheaders/types/simple.h
  moved changes into src/gromacs/utility/real.h
- src/gromacs/gmxlib/network.c &
  src/gromacs/utility/basenetwork.cpp
  changes to network.c partially applied to itself
  and paritally to basenetwork.
- src/gromacs/legacyheaders/network.h (trivial)
- src/programs/mdrun/md.cpp (trivial)

Change-Id: Iaeae5bcc691a3fa84978ee261ceb4a5d2aeb4f62