@@ -3716,17 +3716,17 @@ \subsubsection{Method 1: Free sampling}
37163716
37173717\paragraph {Data analysis }
37183718
3719- Once the simulation is over , the density profile shows that the density in the center of the box is
3719+ Once the simulation is complete , the density profile shows that the density in the center of the box is
37203720about two orders of magnitude lower than inside the reservoir (Fig.\, \ref {fig:US-density }).
3721- Then, let us plot $ -R T \ln (\rho /\rho _\mathrm {bulk})$ (i.e.~Eq.\, \eqref {eq:G } where
3721+ Next, we plot $ -R T \ln (\rho /\rho _\mathrm {bulk})$ (i.e.~Eq.\, \eqref {eq:G } where
37223722the pressure ratio $ p/p_\mathrm {bulk}$ is replaced by the density ratio
3723- $ \rho /\rho _\mathrm {bulk}$ assuming the system is an ideal gas) and compare it
3723+ $ \rho /\rho _\mathrm {bulk}$ , assuming the system behaves as an ideal gas) and compare it
37243724with the imposed potential $ U$ from Eq.\, \eqref {eq:U } (Fig.\, \ref {fig:US-FreeSampling }).
3725- The value for the reference density $ \rho _\text {bulk} = 0.0033 ~\text {\AA {}}^{-3}$
3725+ The reference density, $ \rho _\text {bulk} = 0.0033 ~\text {\AA {}}^{-3}$ ,
37263726was estimated by measuring the density of the reservoir from the raw density
37273727profiles. The agreement between the MD results and the imposed energy profile
3728- is reasonable, despite some noise in the central part ( where fewer data points
3729- are available due to the repulsive potential) .
3728+ is reasonable, despite some noise in the central part, where fewer data points
3729+ are available due to the repulsive potential.
37303730
37313731\begin {figure }
37323732\centering
@@ -3756,12 +3756,13 @@ \subsubsection{Method 1: Free sampling}
37563756\end {figure }
37573757
37583758\paragraph {The limits of free sampling }
3759- If we increase the value of $ U_0 $ , the average number of atoms in the central
3760- region will decrease, making it difficult to obtain a good resolution for the free
3761- energy profile. For instance, when we run the same simulation using $ U_0 = 10 \epsilon $ ,
3762- which corresponds to a situation where $ U_0 \approx 10 k_\text {B} T$ , not a single
3763- atom explores the central part of the simulation box during the 8 ns of simulation.
3764- In this case, using an enhanced sampling method is preferred; see the next section.
3759+
3760+ Increasing the value of $ U_0 $ reduces the average number of atoms in the central
3761+ region, making it challenging to achieve good resolution for
3762+ the free energy profile. For example, running the same simulation with $ U_0 = 10 \epsilon $ ,
3763+ corresponding to $ U_0 \approx 10 k_\text {B} T$ , results in no atoms exploring
3764+ the central part of the simulation box during the simulation.
3765+ In such case, employing an enhanced sampling method is recommended, as done in the next section.
37653766
37663767\subsubsection {Method 2: Umbrella sampling }
37673768Umbrella sampling is a biased molecular dynamics method in which additional forces
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