Changed documentation on common errors during minimization

Fixed title of non-converged minimization in common errors to reflect actual error

Added section on non-finite forces to match the new minimization error message added in
changeset I7428fe4e54304b6cd2a9843445fb3c3d2ab7bc9b

Change-Id: I61e8b7e5493b3ca925e92bdb54a62769901ec7e5

diff --git a/docs/user-guide/run-time-errors.rst b/docs/user-guide/run-time-errors.rst
index edb34c8201e8dcf3b048e384ab01bc0e0bf713e7..58f5a0dd8deb7573ee5b141cd6a4bec6b30cd6ec 100644 (file)
--- a/docs/user-guide/run-time-errors.rst
+++ b/docs/user-guide/run-time-errors.rst
@@ -414,24 +414,33 @@ number of atoms, causing :ref:`grompp <gmx grompp>` to continue searching for at
 Errors in :ref:`mdrun <gmx mdrun>`
 ----------------------------------
 
-Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-This is not an error as such. It is simply informing you that during the
-energy minimization process
-it reached the limit possible to minimize the structure with your current parameters. It does not
-mean that the system has not been minimized fully, but in some situations that may be the case.
-If the system has a significant amount of water present, then an E\ :sub:`pot` of the order
-of -10\ :sup:`5` to -10\ :sup:`6` (in conjunction with an F\ :sub:`max` between 10
-and 1000 kJ mol\ :sup:`-1` nm\ :sup:`-1`) is typically a reasonable value for
+Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested F\ :sub:`max`
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This may not be an error as such. It is simply informing you that during the energy
+minimization process mdrun reached the limit possible to minimize the structure with your
+current parameters. It does not mean that the system has not been minimized fully, but in
+some situations that may be the case. If the system has a significant amount of water present,
+then an E\ :sub:`pot` of the orderof -10\ :sup:`5` to -10\ :sup:`6` (in conjunction with an
+F\ :sub:`max` between 10 and 1000 kJ mol\ :sup:`-1` nm\ :sup:`-1`) is typically a reasonable value for
 starting most MD simulations from the resulting structure. The most important result is
 likely the value of F\ :sub:`max`, as it describes the slope of the potential energy
 surface, i.e. how far from an energy minimum your structure lies. Only for special
 purposes, such as normal mode analysis type of calculations, it may be necessary to minimize further.
-
 Further minimization may be achieved by using a different energy minimization method or by
 making use of double precision-enabled |Gromacs|.
 
+Energy minimization has stopped because the force on at least one atom is not finite
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This likely indicates that (at least) two atoms are too close in the input coordinates, and
+the forces exerted on each other are greater in magnitude than can be expressed to
+the extent of the precision of |Gromacs|, and therefore minimization cannot proceed. It
+is sometimes possible to minimize systems that have infinite forces with the use
+of soft-core potentials, which scale down the magnitude of Lennard-Jones interactions
+with the use of the |Gromacs| free energy code. This approach is an accepted workflow for
+equilibration of some coarse-grained systems such as Martini.
+
 LINCS/SETTLE/SHAKE warnings
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^