diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 1719d75a5..5f41e9a84 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -2504,16 +2504,32 @@ \end{cvcoptions} -\textbf{Tip: stopping the rotation of a protein.} To stop the + +\paragraph*{Example: stopping the rotation of a protein.} To stop the rotation of an elongated macromolecule in solution (and use an anisotropic box to save water molecules), it is possible to define a colvar with an \texttt{orientation} component, and restrain it through the \texttt{harmonic} bias around the identity rotation, \texttt{(1.0, 0.0, 0.0, 0.0)}. Only the overall orientation of the macromolecule -is affected, and \emph{not} its internal degrees of freedom. The user -should also take care that the macromolecule is composed by a single -chain, or disable \texttt{wrapAll} otherwise. +is affected, and \emph{not} its internal degrees of freedom. \cvnamdonly{In NAMD, the user +should also take care that the macromolecule is composed by a single chain +, or disable \texttt{wrapAll} otherwise.} +\begin{cvexampleinput} +\-colvar~\{\\ +\-~~name~Orient\\ +\-~~orientation~\{\\ +\-~~~~atoms~\{~\ldots~\}\\ +\-~~~~refPositionsFile~reference.pdb\\ +\-~~\}\\ +\-\}\\ +\-\\ +\-harmonic~\{~~~~~~~~~~~~~\#~Define~a~harmonic~restraint\\ +\-~~colvars~Orient~~~~~~~\#~acting~on~colvar~"Orient"\\ +\-~~centers~~(1.0,~0.0,~0.0,~0.0)~~\#~center~the~unit~quaternion~(no~rotation)\\ +\-~~forceConstant~500.0~~~~~~~~~~~~\#~unit~is~energy:~quaternions~are~dimensionless\\ +\-\}\\ +\end{cvexampleinput} \cvsubsubsec{\texttt{orientationAngle}: angle of rotation from reference coordinates.}{sec:cvc_orientationAngle}