@@ -4026,13 +4026,15 @@ \subsubsection{Method 2: Umbrella sampling}
40264026
40274027\paragraph {WHAM algorithm }
40284028
4029- To generate the free energy profile from the particle positions
4030- saved in the \flecmd {umbrella-sampling.i.dat} files,
4031- we use the WHAM~\cite {kumar1992weighted ,kumar1995multidim } algorithm as implemented by Marc Grossfield~\cite {grossfieldimplementation }.
4032- You can download it from \href {http://membrane.urmc.rochester.edu/?page_id=126}{Alan Grossfield}'s
4033- website. The executable called \flecmd {wham} generated by following the instructions
4034- from the website must be placed next to \flecmd {umbrella-sampling.lmp}. To apply
4035- the WHAM algorithm to our simulation, we need a metadata file containing:
4029+ To generate the free energy profile from the particle positions saved in
4030+ the \flecmd {umbrella-sampling.i.dat} files, we use the
4031+ WHAM~\cite {kumar1992weighted ,kumar1995multidim } algorithm as implemented
4032+ by Marc Grossfield~\cite {grossfieldimplementation }. You can download it
4033+ from \href {http://membrane.urmc.rochester.edu/?page_id=126}{Alan
4034+ Grossfield}'s website. The executable called \flecmd {wham} generated
4035+ by following the instructions from the website must be placed next to
4036+ \flecmd {umbrella-sampling.lmp}. To apply the WHAM algorithm to our
4037+ simulation, we need a metadata file containing:
40364038\begin {itemize }
40374039\item the paths to all the data files,
40384040\item the values of $ x_\text {des}$ ,
@@ -4042,7 +4044,7 @@ \subsubsection{Method 2: Umbrella sampling}
40424044and save it next to \flecmd {umbrella-sampling.lmp}. Then, run the WHAM algorithm
40434045by typing the following command in the terminal:
40444046\ begin{lstlisting}
4045- ./wham -30 30 50 1e-8 119.8 0 \
4047+ ./wham units real -30 30 50 1e-8 119.8 0 \
40464048 umbrella-sampling.meta umbrella-sampling.dat
40474049\end {lstlisting }
40484050where -30 and 30 are the boundaries, 50 is the number of bins, 1e-8 is the tolerance,
0 commit comments