Reimplement constant acceleration groups

[alexxy/gromacs.git] / docs / user-guide / mdp-options.rst

diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst
index c9ce3a20a0d95f57c731e13fcc7360ceeb8330ff..a1b96fa84ac135e94694637e732a0e86f0c1580d 100644 (file)
--- a/docs/user-guide/mdp-options.rst
+++ b/docs/user-guide/mdp-options.rst
@@ -2095,15 +2095,15 @@ AWH adaptive biasing
 
    .. mdp-value:: positive
 
-      Share the bias and PMF estimates within and/or between simulations.
-      Within a simulation, the bias will be shared between biases that have the
-      same :mdp:`awh1-share-group` index (note that the current code does not support this).
-      With :mdp-value:`awh-share-multisim=yes` and
-      :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
+      Share the bias and PMF estimates between simulations. This currently
+      only works between biases with the same index. Note that currently
+      sharing within a single simulation is not supported.
+      The bias will be shared across simulations that specify the same
+      value for :mdp:`awh1-share-group`. To enable this, use
+      :mdp-value:`awh-share-multisim=yes` and the :ref:`gmx mdrun` option
+      ``-multidir``.
       Sharing may increase convergence initially, although the starting configurations
       can be critical, especially when sharing between many biases.
-      Currently, the share value should increase with increasing bias index
-      (or be 0).
 
 .. mdp:: awh1-ndim
 
@@ -3023,6 +3023,23 @@ Expanded Ensemble calculations
 Non-equilibrium MD
 ^^^^^^^^^^^^^^^^^^
 
+.. mdp:: acc-grps
+
+   groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
+   in groups Protein and Sol will experience constant acceleration as
+   specified in the :mdp:`accelerate` line. Note that the kinetic energy
+   of the center of mass of accelarated groups contributes to the kinetic
+   energy and temperature of the system. If this is not desired, make
+   each accelerate group also a separate temperature coupling group.
+
+.. mdp:: accelerate
+
+   (0) [nm ps\ :sup:`-2`]
+   acceleration for :mdp:`acc-grps`; x, y and z for each group
+   (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
+   constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
+   the opposite).
+
 .. mdp:: freezegrps
 
    Groups that are to be frozen (*i.e.* their X, Y, and/or Z position