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lammps-tutorials.tex

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@@ -3716,17 +3716,17 @@ \subsubsection{Method 1: Free sampling}
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\paragraph{Data analysis}
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Once the simulation is over, the density profile shows that the density in the center of the box is
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Once the simulation is complete, the density profile shows that the density in the center of the box is
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about two orders of magnitude lower than inside the reservoir (Fig.\,\ref{fig:US-density}).
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Then, let us plot $-R T \ln(\rho/\rho_\mathrm{bulk})$ (i.e.~Eq.\,\eqref{eq:G} where
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Next, we plot $-R T \ln(\rho/\rho_\mathrm{bulk})$ (i.e.~Eq.\,\eqref{eq:G} where
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the pressure ratio $p/p_\mathrm{bulk}$ is replaced by the density ratio
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$\rho/\rho_\mathrm{bulk}$ assuming the system is an ideal gas) and compare it
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$\rho/\rho_\mathrm{bulk}$, assuming the system behaves as an ideal gas) and compare it
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with the imposed potential $U$ from Eq.\,\eqref{eq:U} (Fig.\,\ref{fig:US-FreeSampling}).
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The value for the reference density $\rho_\text{bulk} = 0.0033~\text{\AA{}}^{-3}$
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The reference density, $\rho_\text{bulk} = 0.0033~\text{\AA{}}^{-3}$,
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was estimated by measuring the density of the reservoir from the raw density
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profiles. The agreement between the MD results and the imposed energy profile
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is reasonable, despite some noise in the central part (where fewer data points
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are available due to the repulsive potential).
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is reasonable, despite some noise in the central part, where fewer data points
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are available due to the repulsive potential.
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\begin{figure}
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\centering
@@ -3756,12 +3756,13 @@ \subsubsection{Method 1: Free sampling}
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\end{figure}
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\paragraph{The limits of free sampling}
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If we increase the value of $U_0$, the average number of atoms in the central
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region will decrease, making it difficult to obtain a good resolution for the free
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energy profile. For instance, when we run the same simulation using $U_0 = 10 \epsilon$,
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which corresponds to a situation where $U_0 \approx 10 k_\text{B} T$, not a single
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atom explores the central part of the simulation box during the 8 ns of simulation.
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In this case, using an enhanced sampling method is preferred; see the next section.
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Increasing the value of $U_0$ reduces the average number of atoms in the central
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region, making it challenging to achieve good resolution for
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the free energy profile. For example, running the same simulation with $U_0 = 10 \epsilon$,
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corresponding to $U_0 \approx 10 k_\text{B} T$, results in no atoms exploring
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the central part of the simulation box during the simulation.
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In such case, employing an enhanced sampling method is recommended, as done in the next section.
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\subsubsection{Method 2: Umbrella sampling}
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Umbrella sampling is a biased molecular dynamics method in which additional forces

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