Backport valgrind suppression

Was added to master by 106ca9e6 and is now also required by
Jenkins for 5.0. Unclear what triggered that it is required.

Change-Id: I272600716fc986fe77a03fb86da827ba40d17adf
Fixed typo in cmake warning.

Change-Id: Id096ed65567fa671dce40970948b6435d9c357a0
Removed spurious GLY dihedral in AMBER03.

Fixes #1632

Change-Id: I7302e42558454d546e14d7784077fb72c0dbfad7
Updated some .mdp file variables to use "-" instead of deprecated "_"

In the .mdp file, now a minus sign instead of an underline is
generally used. Some sections of the manual still listed .mdp
variable names in the old notation.

- three manual sections (pulling, enforced rotation and computational
  electrophysiology) now use "-" instead of "_" in .mdp file variable
  names
- updated output of rotation code to reflect this up-to-date notation
- no functional changes are in this patch

Change-Id: I7b00193d3e3d549ce8c9a728b307280c0bdd35ce
Fix DD bonded interaction range print

A recent fix caused the DD setup printing of the maximum bonded
distance to instead print the max of the bonded and the list buffer
to the log file. This was a printing issue only.
Refs #1607.

Change-Id: I685e2e5e07f2f1a0a39c5eef4264a77ddfcecb31
Corrected parameter for sorting on search grid

The nbnxn grid search sorting range parameter used the whole box
height instead of the local DD cell height with domain decomposition
along z. This could not cause errors, but the search used O(N^2) time
with more than 4 domains along z, instead of O(N).

Change-Id: I324df6b15635a5ecff7c8bfeb124fdb933e5f845
When writing TNG the input must contain molecule data.

When using trjcat to write TNG the input must also be TNG since
no tpr file is used.

Fixes #1626

Change-Id: I060e0174f9a471e134a4a899f83afaf02f4fce00
Avoid NaN in rlist buffer calculation

With constraints on large masses and very low tolerance, the Verlet
buffer calculation could produce 1/0. This could lead to a somewhat
too smaller buffer.
Also added a missing scaling factor to the contribution of the third
derivative of the potential. This issue only caused a minor
overestimate for systems with constraints and without electrostatics.

Change-Id: I97e9d428a83f1b4954012ebd39bc49d397574f8c
Fixed twin-range + freeze + constraints

With twin-range cut-offs, atoms which are both frozen and constrained
would experience very large or NaN forces, leading to constraint
warnings and errors.
Fixes #1639.

Change-Id: I1871a87054fec1149c9ed75872451df79a8ac2d2
Move code to domdec module folder

It's not a module yet, but here's where it will be. Updated
suppressions for module cyclic dependency warnings for domdec and
mdlib.

Change-Id: Ibe449ec8078fb7f25c4e95ebae28bac74db4f577
Merge release-5-0 into master

Conflicts:
	src/gromacs/mdlib/domdec.cpp (std::max)

Change-Id: Iaa77c561f52cf5815c35cb08008cf578d1be2314
Fix trjconv modifying fr.time unnecessarily

The was a bug where trjconv modified the input frame time, which
caused issues with xtc seeking. This has recently been fixed
by commit 81d10b25, but it's better not to mess with the input
frame and only modify the output frame.

Refs #1405, #1406

Change-Id: Ibf7c8655e916c12f8cc51523a67556cc7988e6e6
Add some unit tests for surface area calculation

There are a few real unit tests that compare the results against
analytical calculation for trivial cases, but the rest of the tests are
more of regression tests, designed to catch changes in the output.
I have not actually checked that the reference values for the more
complex values are correct.

Put the tests in surfacearea.cpp instead of nsc.cpp and renamed the
implementation to match in preparation for future cleanup.

The volume computation with PBC is not tested, since it is broken.

Change-Id: I18e3baa899b1c10fec0c8b43d8dd76a357297005
Convert surface area calculation to C++

Minimal conversion to make min/max work, and remove a few unused
variables.  This enables writing a C++ wrapper over the functionality,
as well as using the analysis neighborhood search internally to fix
several issues with the original algorithm.

Change-Id: If5089a749c8db9630e33edab3d2b79968a28a921
Fix clang with boost 1.46.1 and 1.47

Change-Id: I53b9fcb1bcf553ea128f7edb2d15bec87fd4f9e9
Merge release-5-0 into master

Change-Id: If41f9c458e5d3aa5f841afcd71bc7f72a1f312c7
Further insert-molecules cleanup

- Run insert-molecules tests under valgrind, and fix (most) memory
  leaks.
- Clarify memory management by moving memory allocation of some arrays
  into functions where they are actually used.
- More sensible status output.
- Additional tests.

Change-Id: I7bc2f7b4b155ac650235da00b414561b963d347c
More control over file backups

Add a gmx_set_max_backup_count() to specify how many backups should be
made, instead of just relying on the environment variable.  Make the
default to be no backups: now tests and FAHCORE do not need special
treatment.  Instead, make the command-line initialization specify the
maximum backup count, and add a command-line option that also allows
disabling backups as an alternative to the environment variable.

This also allows removing a valgrind suppression for memory leaks from
the test code.

Change-Id: Ib512eb2a491691c76404aacbf93b67087a1afe41
Merge "Merge release-5-0 into master"
Port gmx-solvate tests to use CommandLineTestBase

This makes the tests relatively easily extendable to support checking
the output.

Change-Id: Icf835aa143d3832a340d156327c0aee6c80ef4ea