version 1.29 | version 1.30 |
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} | } |
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\paragraph*{Usage for multiple--replica eABF.} | \paragraph{Usage for multiple--replica eABF.} |
The eABF algorithm can be associated with a multiple--walker strategy \cite{Minoukadeh2010,Comer2014c} (\ref{sec:mw-ABF}). | The eABF algorithm can be associated with a multiple--walker strategy \cite{Minoukadeh2010,Comer2014c} (\ref{sec:mw-ABF}). |
To run a multiple--replica eABF simulation, start a multiple-replica | To run a multiple--replica eABF simulation, start a multiple-replica |
NAMD run (option \texttt{+replicas}) and set {\tt shared on} in the Colvars config file to enable | NAMD run (option \texttt{+replicas}) and set {\tt shared on} in the Colvars config file to enable |
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\item \dupkey{outputEnergy}{\texttt{histogramRestraint}}{sec:colvarbias}{biasing and analysis methods} | \item \dupkey{outputEnergy}{\texttt{histogramRestraint}}{sec:colvarbias}{biasing and analysis methods} |
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\item % | \item % |
\key % | \key |
{lowerBoundary}{% | {lowerBoundary}{% |
\texttt{histogramRestraint}}{% | \texttt{histogramRestraint}}{% |
Lower boundary of the colvar grid}{% | Lower boundary of the colvar grid}{% |
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\simkey{upperBoundary}{\texttt{histogramRestraint}}{lowerBoundary} | \simkey{upperBoundary}{\texttt{histogramRestraint}}{lowerBoundary} |
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\item % | \item % |
\key % | \key |
{width}{% | {width}{% |
\texttt{histogramRestraint}}{% | \texttt{histogramRestraint}}{% |
Width of the colvar grid}{% | Width of the colvar grid}{% |
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} | } |
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\item % | \item % |
\keydef% | \keydef |
{gaussianSigma}{% | {gaussianSigma}{% |
\texttt{histogramRestraint}}{% | \texttt{histogramRestraint}}{% |
Standard deviation of the approximating Gaussian}{% | Standard deviation of the approximating Gaussian}{% |
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} | } |
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\item % | \item % |
\key% | \key |
{refHistogram}{% | {refHistogram}{% |
\texttt{histogramRestraint}}{% | \texttt{histogramRestraint}}{% |
Reference histogram $h_{0}(\xi)$}{% | Reference histogram $h_{0}(\xi)$}{% |
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} | } |
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\item % | \item % |
\key% | \key |
{refHistogramFile}{% | {refHistogramFile}{% |
\texttt{histogramRestraint}}{% | \texttt{histogramRestraint}}{% |
Reference histogram $h_{0}(\xi)$}{% | Reference histogram $h_{0}(\xi)$}{% |