diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp index fc019fc3b88ad2990978d43006c3bc8a917c2b1c..9ea684e6bed4deb4ce484ef354b352ade5aaa68d 100644 --- a/src/bias/MetaD.cpp +++ b/src/bias/MetaD.cpp @@ -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. @@ -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. @@ -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.