| version 1.32 | version 1.33 |
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| \cvsubsec{Harmonic wall restraints} | \cvsubsec{Harmonic wall restraints} |
| \label{sec:colvarbias_harmonic_walls} | \label{sec:colvarbias_harmonic_walls} |
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| The \texttt{harmonicWalls~\{...\}} bias is closely related to the harmonic bias (see \ref{sec:colvarbias_harmonic}), with the following two differences: \emph{(i)} instead of a center a \emph{lower wall} and/or an \emph{upper wall} are defined, outside odf which the bias implements a half-harmonic potential; | The \texttt{harmonicWalls~\{...\}} bias is closely related to the harmonic bias (see \ref{sec:colvarbias_harmonic}), with the following two differences: \emph{(i)} instead of a center a \emph{lower wall} and/or an \emph{upper wall} are defined, outside of which the bias implements a half-harmonic potential; |
| \begin{equation} | \begin{equation} |
| \label{eq:colvarbias_harmonic_walls} | \label{eq:colvarbias_harmonic_walls} |
| V(\xi) = \left\{ | V(\xi) = \left\{ |
| |
| \end{array} | \end{array} |
| \right. | \right. |
| \end{equation} | \end{equation} |
| where $\xi_{\mathrm{lower}}$ and $\xi_{\mathrm{upper}}$ are the lower and upper wall thresholds, respectively; \emph{(ii)} because an interval between two walls is defined, only scalar variables can be used (but any number of variables can be deined, and the wall bias is intrinsically multi-dimensional). | where $\xi_{\mathrm{lower}}$ and $\xi_{\mathrm{upper}}$ are the lower and upper wall thresholds, respectively; \emph{(ii)} because an interval between two walls is defined, only scalar variables can be used (but any number of variables can be defined, and the wall bias is intrinsically multi-dimensional). |
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| \textbf{Note:} this bias replaces the keywords \texttt{lowerWall}, \texttt{lowerWallConstant}, \texttt{upperWall} and \texttt{upperWallConstant} defined in the \texttt{colvar} context (see \ref{sec:colvar}). | \textbf{Note:} this bias replaces the keywords \texttt{lowerWall}, \texttt{lowerWallConstant}, \texttt{upperWall} and \texttt{upperWallConstant} defined in the \texttt{colvar} context (see \ref{sec:colvar}). |
| These keywords are still supported, but will be deprecated in the future. | These keywords are still supported, but will be deprecated in the future. |
| |
| Defines the values $\xi_{\mathrm{upper}}$ ve which a confining restraint on the colvar is applied to each colvar $\xi$.} | Defines the values $\xi_{\mathrm{upper}}$ ve which a confining restraint on the colvar is applied to each colvar $\xi$.} |
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| \item \dupkey{forceConstant}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} | \item \dupkey{forceConstant}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |
| \textbf{Note:} if two distinct force constants are needed for the two walls, it is possible to define a \texttt{harmonicWalls} instance for each. | % \textbf{Note:} if two distinct force constants are needed for the two walls, it is possible to define a \texttt{harmonicWalls} instance for each. |
| | |
| | \item % |
| | \keydef |
| | {lowerWallConstant}{% |
| | \texttt{harmonicWalls}}{% |
| | Force constant for the lower wall}{% |
| | positive decimal}{% |
| | \texttt{forceConstant}}{% |
| | When both sets of walls are defined (lower and upper), this keyword allows setting different force constants for them. |
| | The force constant reported in the output as ``$k$'', and used in the change of force constant scheme, is the geometric mean of the two. |
| | } |
| | |
| | \item % |
| | \simkey{upperWallConstant}{\texttt{harmonicWalls}}{lowerWallConstant} |
| | |
| \item \dupkey{targetForceConstant}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} | \item \dupkey{targetForceConstant}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |
| \item \dupkey{targetNumSteps}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} | \item \dupkey{targetNumSteps}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |