Update documention of Nose-Hoover output

The documentation of Nose-Hoover chain variable printing was
(long) outdated.

Refs #2301

Change-Id: I2ef02e676141000937fedecf096b635ee2e69281

diff --git a/docs/manual/algorithms.tex b/docs/manual/algorithms.tex
index 9fbd45c28f341ee6512bcca6761227a8185ea7d0..a12c7f3ffe164e33629a3ed2301b7cb3df17800d 100644 (file)
--- a/docs/manual/algorithms.tex
+++ b/docs/manual/algorithms.tex
@@ -1337,12 +1337,11 @@ H = \sum_{i=1}^{N} \frac{\pb_i}{2m_i} + U\left(\rv_1,\rv_2,\ldots,\rv_N\right) +
 The values and velocities of the Nos{\'e}-Hoover thermostat variables
 are generally not included in the output, as they take up a fair
 amount of space and are generally not important for analysis of
-simulations, but this can be overridden by defining the environment
-variable {\tt GMX_NOSEHOOVER_CHAINS}, which will print the values of all
+simulations, but by setting an mdp option the values of all
 the positions and velocities of all Nos{\'e}-Hoover particles in the
-chain to the {\tt .edr} file.  Leap-frog simulations currently can only have 
-Nos{\'e}-Hoover chain lengths of 1, but this will likely be updated in 
-later version.
+chain are written to the {\tt .edr} file.  Leap-frog simulations
+currently can only have  Nos{\'e}-Hoover chain lengths of 1,
+but this will likely be updated in later version.
 
 As described in the integrator section, for temperature coupling, the
 temperature that the algorithm attempts to match to the reference

diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst
index 3feb1d2737639dd4ad6cc6f7a95f5723138fb50a..4284cd77b18e905544dfc4ae02638ddb1655fe2b 100644 (file)
--- a/docs/user-guide/mdp-options.rst
+++ b/docs/user-guide/mdp-options.rst
@@ -1048,9 +1048,20 @@ Temperature coupling
    (10)
    The number of chained Nose-Hoover thermostats for velocity Verlet
    integrators, the leap-frog :mdp-value:`integrator=md` integrator
-   only supports 1. Data for the NH chain variables is not printed to
-   the :ref:`edr` file, but can be using the ``GMX_NOSEHOOVER_CHAINS``
-   environment variable
+   only supports 1. Data for the NH chain variables is not printed
+   to the :ref:`edr` file by default, but can be turned on with the
+   :mdp:`print-nose-hoover-chains` option.
+
+.. mdp:: print-nose-hoover-chain-variables
+
+   .. mdp-value:: no
+
+      Do not store Nose-Hoover chain variables in the energy file.
+
+   .. mdp-value:: yes
+
+      Store all positions and velocities of the Nose-Hoover chain
+      in the energy file.
 
 .. mdp:: tc-grps