Add support for transformation pull coordinates

[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 beb3f2972be11326ce9ba294853b9a92556aa9fc..590b5425e17ce78456e0105ddfdcc0959719563d 100644 (file)
--- a/docs/user-guide/mdp-options.rst
+++ b/docs/user-guide/mdp-options.rst
@@ -1792,6 +1792,29 @@ pull-coord2-vec, pull-coord2-k, and so on.
       then defined as the angle between two planes: the plane spanned by the
       the two first vectors and the plane spanned the two last vectors.
 
+   .. mdp-value:: transformation
+
+      Transforms other pull coordinates using a mathematical expression defined by :mdp:`pull-coord1-expression`.
+      Pull coordinates of lower indices can be used as variables to this pull coordinate.
+      Thus, pull transformation coordinates should have a higher pull coordinate index
+      than all pull coordinates they transform.
+
+.. mdp:: pull-coord1-expression
+
+   Mathematical expression to transform pull coordinates of lower indices to a new one.
+   The pull coordinates are referred to as variables in the equation so that
+   pull-coord1's value becomes 'x1', pull-coord2 value becomes 'x2' etc.
+   The mathematical expression are evaluated using muParser.
+   Only relevant if :mdp:`pull-coord1-geometry` is set to :mdp-value:`transformation`.
+
+.. mdp:: pull-coord1-dx
+
+   (1e-9)
+   Size of finite difference to use in numerical derivation of the pull coordinate
+   with respect to other pull coordinates.
+   The current implementation uses a simple first order finite difference method to perform derivation so that
+   f'(x) = (f(x+dx)-f(x))/dx
+   Only relevant if :mdp:`pull-coord1-geometry` is set to :mdp-value:`transformation`.
 
 .. mdp:: pull-coord1-groups