| version 1.31 | version 1.32 |
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| |
| | % This file is part of the Collective Variables module (Colvars). |
| | % The original version of Colvars and its updates are located at: |
| | % https://github.com/colvars/colvars |
| | % Please update all Colvars source files before making any changes. |
| | % If you wish to distribute your changes, please submit them to the |
| | % Colvars repository at GitHub. |
| | |
| \cvnamdugonly{ | \cvnamdugonly{ |
| \section{Collective Variable-based Calculations (Colvars)\footnote{The features described in this section were contributed by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and J\'er\^ome H\'enin (IBPC, CNRS, Paris, France). Please send feedback and suggestions to the NAMD mailing list.}} | \section{Collective Variable-based Calculations (Colvars)\footnote{The features described in this section were contributed by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and J\'er\^ome H\'enin (IBPC, CNRS, Paris, France). Please send feedback and suggestions to the NAMD mailing list.}} |
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| \end{itemize} | \end{itemize} |
| | |
| | |
| \cvsubsec{Artificial boundary potentials (walls)} | |
| | |
| The following options are useful to define restraints (confining potentials) for this colvar. | |
| To apply moving restraints, or restraints to more than one colvar simultaneously, a more convenient option is to use the \texttt{harmonic} bias (\ref{sec:colvarbias_harmonic}). | |
| | |
| \begin{itemize} | |
| | |
| \item % | |
| \key | |
| {lowerWallConstant}{% | |
| \texttt{colvar}}{% | |
| Lower wall force constant (\cvnamdonly{kcal/mol/U$^2$}\cvvmdonly{kcal/mol/U$^2$}\cvlammpsonly{unit of energy specified by \texttt{units}})}{% | |
| positive decimal}{% | |
| Defines the force constant for a confining restraint on the colvar, in the form of a ``half-harmonic'' potential. | |
| The potential starts at \texttt{lowerWall} if it is defined, or \texttt{lowerBoundary} otherwise. | |
| The energy unit of the constant is \cvnamdonly{kcal/mol}\cvvmdonly{kcal/mol}\cvlammpsonly{the unit of energy specified by \texttt{units}}, while the spatial unit U is that of the colvar.} | |
| | |
| \item % | |
| \keydef | |
| {lowerWall}{% | |
| \texttt{colvar}}{% | |
| Position of the lower wall}{% | |
| decimal}{% | |
| \texttt{lowerBoundary}}{% | |
| Defines the value below which a confining restraint on the colvar is applied, in the form of a ``half-harmonic'' potential. | |
| Allows to use a different position of the wall than \texttt{lowerBoundary}.} | |
| | |
| \item % | |
| \key | |
| {upperWallConstant}{% | |
| \texttt{colvar}}{% | |
| Upper wall force constant (\cvnamdonly{kcal/mol/U$^2$}\cvvmdonly{kcal/mol/U$^2$}\cvlammpsonly{unit of energy specified by \texttt{units}})}{% | |
| positive decimal}{% | |
| Analogous to \texttt{lowerWallConstant}.} | |
| | |
| \item % | |
| \keydef | |
| {upperWall}{% | |
| \texttt{colvar}}{% | |
| Position of the upper wall}{% | |
| decimal}{% | |
| \texttt{upperBoundary}}{% | |
| Analogous to \texttt{lowerWall}.} | |
| \end{itemize} | |
| | |
| | |
| \cvsubsec{Trajectory output} | \cvsubsec{Trajectory output} |
| | |
| \begin{itemize} | \begin{itemize} |
| |
| boolean}{% | boolean}{% |
| \texttt{off}}{% | \texttt{off}}{% |
| If \texttt{colvarsTrajFrequency} is defined, the total force | If \texttt{colvarsTrajFrequency} is defined, the total force |
| applied on this colvar by biases and confining potentials (walls) | applied on this colvar by Colvars biases are |
| within the Colvars module are | |
| written to the trajectory under the label | written to the trajectory under the label |
| ``\texttt{fa\_}$<$\texttt{name}$>$''. | ``\texttt{fa\_}$<$\texttt{name}$>$''. |
| For extended Lagrangian colvars, this force is actually applied to the | For extended Lagrangian colvars, this force is actually applied to the |
| |
| \item % | \item % |
| \dupkey{group1}{\texttt{selfCoordNum}}{colvar|coordNum|group1}{\texttt{coordNum} component} | \dupkey{group1}{\texttt{selfCoordNum}}{colvar|coordNum|group1}{\texttt{coordNum} component} |
| \item % | \item % |
| \simkey{group2}{\texttt{selfCoordNum}}{group1} | |
| \item % | |
| \dupkey{cutoff}{\texttt{selfCoordNum}}{colvar|coordNum|cutoff}{\texttt{coordNum} component} | \dupkey{cutoff}{\texttt{selfCoordNum}}{colvar|coordNum|cutoff}{\texttt{coordNum} component} |
| \item % | \item % |
| \dupkey{cutoff3}{\texttt{selfCoordNum}}{colvar|coordNum|cutoff3}{\texttt{coordNum} component} | \dupkey{cutoff3}{\texttt{selfCoordNum}}{colvar|coordNum|cutoff3}{\texttt{coordNum} component} |
| |
| | |
| \end{itemize} | \end{itemize} |
| | |
| | |
| | \cvsubsec{Harmonic wall restraints} |
| | \label{sec:colvarbias_harmonic_walls} |
| | |
| | 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; |
| | \begin{equation} |
| | \label{eq:colvarbias_harmonic_walls} |
| | V(\xi) = \left\{ |
| | \begin{array}{l l} |
| | \frac{1}{2} k \left(\frac{\xi - \xi_{\mathrm{upper}}}{w_{\xi}}\right)^2 & \mathrm{if }\ \xi > \xi_{\mathrm{upper}} \\ |
| | 0 & \mathrm{if }\ \xi_{\mathrm{lower}} \leq \xi \geq \xi_{\mathrm{upper}} \\ |
| | \frac{1}{2} k \left(\frac{\xi - \xi_{\mathrm{lower}}}{w_{\xi}}\right)^2 & \mathrm{if }\ \xi < \xi_{\mathrm{lower}} |
| | \end{array} |
| | \right. |
| | \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). |
| | |
| | \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. |
| | |
| | The \texttt{harmonicWalls} bias implements the following options: |
| | \begin{itemize} |
| | \item \dupkey{name}{\texttt{harmonicWalls}}{sec:colvarbias}{biasing and analysis methods} |
| | \item \dupkey{colvars}{\texttt{harmonicWalls}}{sec:colvarbias}{biasing and analysis methods} |
| | \item \dupkey{outputEnergy}{\texttt{harmonicWalls}}{sec:colvarbias}{biasing and analysis methods} |
| | |
| | \item % |
| | \key |
| | {lowerWalls}{% |
| | \texttt{colvar}}{% |
| | Position of the lower wall}{% |
| | Space-separated list of decimals}{% |
| | Defines the values $\xi_{\mathrm{lower}}$ below which a confining restraint on the colvar is applied to each colvar $\xi$.} |
| | |
| | \item % |
| | \key |
| | {upperWalls}{% |
| | \texttt{colvar}}{% |
| | Position of the lower wall}{% |
| | Space-separated list of decimals}{% |
| | Defines the values $\xi_{\mathrm{upper}}$ ve which a confining restraint on the colvar is applied to each colvar $\xi$.} |
| | |
| | \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. |
| | |
| | \item \dupkey{targetForceConstant}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |
| | \item \dupkey{targetNumSteps}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |
| | \item \dupkey{targetForceExponent}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |
| | \item \dupkey{targetEquilSteps}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |
| | \item \dupkey{targetNumStages}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |
| | \item \dupkey{lambdaSchedule}{\texttt{harmonicWalls}}{sec:colvarbias_harmonic}{Harmonic restraints} |
| | |
| | \end{itemize} |
| | |
| | |
| | |
| \cvsubsec{Linear restraints} | \cvsubsec{Linear restraints} |
| \label{sec:colvarbias_linear} | \label{sec:colvarbias_linear} |
| | |