From: Berk Hess Date: Fri, 24 Sep 2021 14:52:47 +0000 (+0000) Subject: Add manual subsection for transformation pull coord X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=5402185c50648a61c80d7621b16fe23e3a50905e;p=alexxy%2Fgromacs.git Add manual subsection for transformation pull coord --- diff --git a/docs/reference-manual/special/pulling.rst b/docs/reference-manual/special/pulling.rst index 1d481a8b2c..fcc7042171 100644 --- a/docs/reference-manual/special/pulling.rst +++ b/docs/reference-manual/special/pulling.rst @@ -68,6 +68,11 @@ linearly changing with time. value. This is useful for restraining e.g. the distance between two molecules to a certain region. +#. **External potential** This takes the potential acting on the reaction + coordinate from another module. Current only the Accelerated Weight + Histogram method (see sec. :doc:`awh`) is supported, which provides + adaptive biasing of pull coordinates. + In addition, there are different types of reaction coordinates, so-called pull geometries. These are set with the :ref:`mdp` option ``pull-coord?-geometry``. @@ -238,6 +243,30 @@ vector from group 1 to 5, and the third vector is the COM distance vector from group 5 to 9. The dihedral angle takes values in the interval (-180, 180] deg and has periodic boundaries. +The transformation pull coordinate +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The transformation pull coordinate is a "meta" pull coordinate type that +can transform one or more other pull coordinates using an arbitrary +mathematical expression. This is a powerful tool for generating +complex reaction coordinates like a contact coordinate +using a non-linear transformation of a distance, a sum of contacts or +arbitrary (non-)linear combinations of two or more pull coordinates. +A simple example is a contact coordinate using a non-linear transformation +of a distance. More complex examples are a (non-)linear combination of +two or more pull coordinates or a sum of contacts. + +Typically, the force constant for pull coordinate(s) the transformation +coordinates acts on should be zero. This avoids +unintended addition of direct forces on the pull coordinate(s) +to the indirect forces from the transition pull coordinate. This is not +a requirement, but have both a direct and indirect, from the tranformation +coordinate, force working on them is almost never desirable. +If the transformation is a linear combination of multiple distances, +it is useful to normalize the coefficients +such that the transformation coordinate also has units of nanometer. +That makes both the choice of the force constant and the interpretation easier. + Limitations ^^^^^^^^^^^