Fix pdb2gmx -cmap in corner cases

CMAP torsions are only generated when the atoms are from the same chain
(pdb2gmx -merge allows multiple chains to be present in the
moleculetype), and their residues are in residuetypes.dat as
"Protein".

Fixes #800, #885

Change-Id: Idc4f9a867beedc0be6a4c153606c0731eec86f5f
Minor formatting fixes to .mdp option documentation

Change-Id: I71762463880e4cb650f680a2ed83125e450f003a
Merge "Minor formatting fixes to .mdp option documentation" into release-4-5-patches
use separate PME nodes with #nodes>18

PME nodes were used with #nodes>=10, but with 2D PME decomposition,
introduced already in 4.5, PME nodes are not faster with 12 or 16 nodes.

Change-Id: I9c5c8ac225df9d4b81f451074b74d35f002205ee
fixed array index out of bounds in EM force trr storage

The partially implemented force copy was a leftover from a different way
of copying, which should never have been committed.

Change-Id: I026aa79158afcc327185f2f0cf6167d040eccede
Merge branch 'release-4-5-patches' into release-4-6

Also fixed uninitialized variable warning in pdb2top.c with gcc 4.3.

Conflicts:
	share/html/online/mdp_opt.html

Change-Id: I8e499a77a3ce71c2063f453348330e2aad38669b
[tools] Move common functions from gmx_sans.c to nsfactor.c

This commit moves common functions to gmx_sans and gmx_nse to nsfcator.c

Change-Id: Ifcf8e87203dd8721bb91807cd96d0e21f797b918
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Minimal support for Clang

Change-Id: I4c6fb22ef8b5d596527eb8fe0991c3c573be606c
removed initial temperature with OpenMM, fixes #757

Change-Id: Ifc661ce3ece3dfcd2e4bad862392b96d64e70c18
added check for mass-weighting with g_anaeig -entropy, fixes #785

Change-Id: I7a1623ba7a7c7987078901876fb4717d8c0a7261
fixed g_anaeig incorrect multiple extremes, fixes #870

Change-Id: Id06f267c1da300f2a940778833ec35b85fecd3f1
Merge "Minimal support for Clang" into release-4-5-patches
Improve FindFFTW

* mark internally used variables INTERNAL
* make pkg-config search quiet on 2nd run to avoid confusion

Change-Id: I8b91adea1af8a14dffb88438fb2620df738f5a76
Improved cryptic error message

Change-Id: Idd3f7a9ce36e155c61009b16da9a1f2b1a98e93e
Made description string for g_select -select clearer

New UNIX users wouldn't guess they had to enclose the selection
string in quotes to get around their shell.

Change-Id: I8dd7fdd237e4290ad830a168b4880739aa5dc425
Improved warning note with DD and periodic molecules

Change-Id: I3f7f201edcce1b70a360d0462e5103dfc144b2d7
Make finite checks remember theirs results

* saves time on rerun of cmake
* makes cmake quiet on rerun

Change-Id: I2120d8f13d2b7c5baa52d5aa8f06d6eb9ca2bb26
Editorial changes to tools documentation

Made LaTeX type-setting of maths in documentation of tools more
sophisticated, without changing the presentation of maths in
plain text mode.

Various spelling and typographical fixes also.

Change-Id: Ia0c13e1f2ba825911c6e0673af6b940aba9efa21
More editorial fixes to tool documentation

Needed to add better treatment of <averages> and
|magnitudes| for LaTeX versions.

Change-Id: I5e8e3a8d685715af38117a762327d41a8bedf391
Merge "Improved warning note with DD and periodic molecules" into release-4-5-patches