Document correct comm_mode option

Change-Id: I18d9896c51d486dfcc52e4d15b052d65de91426d
Improved pdb2gmx output

Now there is explicit feedback that pdb2gmx is starting generating
hydrogens and termini, which can help the user deduce that problems
lie with those databases, and not necessarily the residue topology
database.

Change-Id: Ie4100b8586d6389a6965ea8cb09eb24cc4e7d3d9
Merge "Improved pdb2gmx output" into release-4-5-patches
Merge "Document correct comm_mode option" into release-4-5-patches
Fixed .g96 trajectory reading.

The line variable in .g96 configuration reading can now be made
persistent - and is done so for reading .g96 trajectories.

This commit fixes #781

Change-Id: If2005a00bb925b41802c4b0dc92e66eb5635f22c
Made tutorial slightly less confusing.

Change-Id: Ief3132a54770e8b3c3b69b24b5582ba321ccc5fd
Merge "Fixed .g96 trajectory reading." into release-4-5-patches
Adapted NMR related data to new pdb format.

Since gromacs had adopted the pdb output format to
some standard, the script to convert xplor files
with NMR restratints, such as can be downloaded from
the pdb do not work anymore. The script and accompanying
table have been updated to work with the new pdb format
and simultaneously the extra argument for a residue offset
has been removed. Now the script can be run like
xplor2gmx.pl conf.pdb < restraints.md > disre.itp

Change-Id: I7c3c8bd49b002e2bf0760f4226c913aa36d64611
Corrected REMD citation

The Fukushima paper relates exclusively to MC and spin glasses.

Change-Id: I58c4eafbe41b0cbd1f3e4afac6f34458ed27eea2
Fix some memory leaks.

Fixes part of #1004.

Change-Id: I22280999c5c3c40e8efae45461bd53bae8e2ff40
Backport of md-vv rerun check from c7a82654f2eb8992

Rerun in parallel with md-vv is broken. The check was added
in c7a82654f2eb8992 but also affects 4.5.

Fixes #1003

Change-Id: Ie0e200a8328b2baecd2eba9eea1453c65a668633
fixed recent bug with grompp check for P-R P-coupling

Fix for recent commit 57dac834

Change-Id: I5bc631d6db848c8702a65c42ae27f096804abbf7
Merge "fixed recent bug with grompp check for P-R P-coupling" into release-4-5-patches
Merge "Adapted NMR related data to new pdb format." into release-4-5-patches
Merge "Fix some memory leaks." into release-4-5-patches
Fix insolidangle selections near poles.

- Correctly treat cases where a point is so close the one of the poles
  that it completely covers one or more bins in the zenith angle
  direction.
- Adjust update_surface_bin() to be more robust to rounding errors and
  easier to understand by simplifying the code used for wrapping angles
  to [-pi, pi] interval.  Problems were triggered here by the first
  change.
- Update comments.

Fixes #1004.

Change-Id: I2707f775793fabb64ea197bdae5fbfe68d6a8933
Fixes for numeric and position selection variables.

Fixed handling of numeric and position selection variables in cases
where they were referenced multiple times.

Backported from Ifbb585ca.

Fixes #1006.

Change-Id: Ieaa479b4b870e044dc269339be57f6b33533c46e
Fix REMD use of gmx_large_int_t for #steps variable

Change-Id: I0a72a8b838de4d018c2715f9d620a86134969206
Add pdbname selection keyword.

As a supporting change, remove trailing space from t_pdbinfo.atomnm, as
the trailing whitespace does not seem to be used anywhere.
This makes it possible to use it easily in the selection code.

Fixes #1007; fix backported from Iac36bda8.

Also includes changes from 8bddac3 to make the backport easier.

Change-Id: Iac36bda8a84d0a6c131445e7f47ad91d7209fb10
Merge "Fix REMD use of gmx_large_int_t for #steps variable" into release-4-5-patches