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Small fix to eABF documentation
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Recommend tighter coupling, empirically better, bypasses CZAR shortcomings.
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jhenin committed Nov 14, 2024
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At long simulation times, eABF produces a flat histogram of the extended variable $\lambda$,
and a flattened histogram of $\xi$, whose exact shape depends on the strength of the coupling
as defined by \texttt{extendedFluctuation} in the colvar.
Coupling should be somewhat loose for faster exploration and convergence, but strong
enough that the bias does help overcome barriers along the colvar $\xi$.\cite{Lesage2017}
Coupling should be strong enough that the bias helps overcome barriers along the colvar.\cite{Lesage2017}
A value of \texttt{extendedFluctuation} equal to the bin width is often reasonable.
In the limit of strong coupling (small \texttt{extendedFluctuation}), the eABF free energy surface
(\texttt{.pmf} file) becomes close to the true one, making the asymptotically more accurate but
noisier CZAR estimator (\texttt{.czar.pmf} file) unnecessary.
In practice, we recommend comparing these two free energy surfaces to decide which one to use.
Distribution of the colvar may be assessed by plotting its histogram, which
is written to the \outputName\texttt{.zcount} file in every eABF simulation.
Note that a \texttt{histogram} bias (\ref{sec:colvarbias_histogram})
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