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Martin Kurečka
Plumed AlphaFold
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22075e09
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Commit
22075e09
authored
6 years ago
by
Michele Invernizzi
Committed by
Giovanni Bussi
6 years ago
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deleted extra '\' causing wrong view in doc
Closes #426
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src/bias/MetaD.cpp
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22075e09
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@@ -135,16 +135,16 @@ for replica exchange methods to be computed correctly.
Multiple walkers \cite multiplewalkers can also be used. See below the examples.
The
\
\f$c(t)\
\
f$ reweighting factor can also be calculated on the fly using the equations
The \f$c(t)\f$ reweighting factor can also be calculated on the fly using the equations
presented in \cite Tiwary_jp504920s.
The expression used to calculate
\
\f$c(t)\
\
f$ follows directly from Eq. 3 in \cite Tiwary_jp504920s,
where
\
\f$F(\vec{s})=-\gamma/(\gamma-1) V(\vec{s})\
\
f$.
The expression used to calculate \f$c(t)\f$ follows directly from Eq. 3 in \cite Tiwary_jp504920s,
where \f$F(\vec{s})=-\gamma/(\gamma-1) V(\vec{s})\f$.
This gives smoother results than equivalent Eqs. 13 and Eqs. 14 in that paper.
The
\
\f$c(t)\
\
f$ is given by the rct component while the bias
normalized by
\
\f$c(t)\
\
f$ is given by the rbias component (rbias=bias-rct) which can be used
The \f$c(t)\f$ is given by the rct component while the bias
normalized by \f$c(t)\f$ is given by the rbias component (rbias=bias-rct) which can be used
to obtain a reweighted histogram.
The calculation of
\
\f$c(t)\
\
f$ is enabled by using the keyword CALC_RCT.
By default
\
\f$c(t)\
\
f$ is updated every time the bias changes, but if this slows down the simulation
The calculation of \f$c(t)\f$ is enabled by using the keyword CALC_RCT.
By default \f$c(t)\f$ is updated every time the bias changes, but if this slows down the simulation
the keyword RCT_USTRIDE can be set to a value higher than 1.
This option requires that a grid is used.
...
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@@ -233,7 +233,7 @@ one update and the other. Since version 2.2.5, hills files are automatically
flushed every WALKERS_RSTRIDE steps.
\par
The
\
\f$c(t)\
\
f$ reweighting factor can be calculated on the fly using the equations
The \f$c(t)\f$ reweighting factor can be calculated on the fly using the equations
presented in \cite Tiwary_jp504920s as described above.
This is enabled by using the keyword CALC_RCT,
and can be done only if the bias is defined on a grid.
...
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@@ -248,9 +248,9 @@ METAD ...
\endplumedfile
Here we have asked that the calculation is performed every 10 hills deposition by using
RCT_USTRIDE keyword. If this keyword is not given, the calculation will
by default be performed every time the bias changes. The
\
\f$c(t)\
\
f$ reweighting factor will be given
by default be performed every time the bias changes. The \f$c(t)\f$ reweighting factor will be given
in the rct component while the instantaneous value of the bias potential
normalized using the
\
\f$c(t)\
\
f$ reweighting factor is given in the rbias component
normalized using the \f$c(t)\f$ reweighting factor is given in the rbias component
[rbias=bias-rct] which can be used to obtain a reweighted histogram or
free energy surface using the \ref HISTOGRAM analysis.
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