Updated note in manual on stochastic dynamics integrator

The comment in the SD section about Berendsen was outdated. Added a few sentences on equilibration/damping of modes.

Added grompp note for Parrinello-Rahman + position restraints

This combination can be unstable and is often not desirable, so grompp now issues a note to suggest alternatives to the user.

Refs Issue 2330

Clarified the description of Fmax during energy minimization

Improved vsite parallel checking

The vsite struct now stores internally whether it has been configured with domain decomposition. This allows for internal checks on valid commrec, which have now been added, and would have prevented Issue 2257.

Added partial support for writing masses and partial charges with TNG files

Issue 2188

Updated TNG to version 1.8.1

Added data block for atom masses.

Fixes Issue 2187 and Issue 2250 and other bugs and warnings.

Added load balance fraction to DLB print

DLB can often be based on a small fraction of the total step time, especially with GPUs. Now this is printed to md.log and stderr.

Added reference for dihedral function in OPLS.

The OPLS four-term dihedral function was not described in the reference listed earlier, so this was updated. Also updated the reference to the three term dihedral to an older paper.

Updated many aspects of the documentation

Imported and updated more material from the wiki. Incorporated suggestions arising from many Redmine issues. Updated user guide, developer guide, install guide, and reference manual.

Updated mdrun signal help text

Updated mdrun help text on signal handling for old and recent changes to the behavior.

Fixes Issue 2324

Changed to handle erroneous command line args better

Some gmx modules need to be able to accept non-option arguments, and some should not. Introduced enough functionality to support such behaviour, while giving useful error messages in cases where the command line is merely missing hyphens (which can happen e.g. when people copy-paste from inconveniently built PDF files for tutorials). Increased test coverage of relevant cases.

Removed some useless command-line argument strings from test cases that never needed them.

Also tested some behaviours of handling string options, and renamed some test input strings to reflect the intent.

Issue 2153

Changed to no longer allow multiple energy groups for GPU runs

Exit with a fatal error instead of only warning, since the latter leads to writing data for energy groups that is incorrect to the energy file.

Issue 1822

Removed duplications in GMXLIB search paths

Remove entries that are duplicated, or identical to the default search path, to avoid e.g. listing identical force fields multiple times.

Issue 1928

Changed to no longer write reference pull group 0 to log

This is an internal group used for absolute references, which cannot be set by users, so printing it just leads to confusion.

Issue 2143