Finalize change from GMX_CPU_ACCELERATION to GMX_SIMD

Change-Id: I6c947d80f36c2fd8e1608520cb505d0586719644
Permit trjconv to read and write velocities with TNG files

Partial fix of #1502

This set velocity reading and writing on for tng file in trjconv.
However there still is a problem with the number of frames being
reduced at each conversion.

Change-Id: I91e7f5245ca75ebb9dd8e4450f94015b5c3f2bfa
Bug fix in the TNG library to improve reading.

Reading single frame frame sets did not work properly.
Fixes #1502 and partial fix of #1510.

Reread frame set after getting stride length.

Extra check to avoid reading past end of file when
checking what data blocks are present.

Change-Id: I5275382bd49b5b46ebfdebe535c53d2f09015bc0
Fix bug writing TNG output from dump.

The output was incorrectly located in an if statement.
Partial fix of #1510

Change-Id: I85823d9369f208f21f4bafe19705e9e4dd2da027
Two quotes contributed by Vedran Miletic

Change-Id: Ib5dfc367c99bba312e669de8db1ddc68f65a9480
Fixed typo in manual

Change-Id: Ic772c4b7bfc2128fff05c1e686999ba739725c53
Add quote on the kT-kj/mol conversion factor

Great advice to all those struggling with remembering numbers by Anders
Gabrielsson.

Change-Id: I65fe5247b9342f6f48de709ad5bdbc69a52abc9a
Added grompp checks for zero atom masses in state B

Grompp already issued fatal errors if atoms had zero mass, or
if vsites had non-zero mass, in state A. This patch adds
state B to the same check.

Refs #1433.

Change-Id: Iec3d764ff7db6e7bdc3901d51b475cf2c35fe137
Use RNG correctly for v-rescale thermostat

Two integers were passed in the wrong order. I suspect from the
construction of the RNG that the only effect of this is to permit a
rare re-use of a random number in a different RNG stream (i.e. no
effect in practice).

Change-Id: I1fb8eddbe7c8b029dc3686be80f3f083108fc28c
Merge release-5-0 into master

Conflicts:
	share/top/gurgle.dat

Change-Id: I95bb9d2ce43ed7fdfe6cfd535e4f88fac9dfb5ea
Merge "Merge release-5-0 into master"