started cleaning tutorial 7

Author: simongravelle

files/tutorial7/solution/free-sampling.lmp

@@ -0,0 +1,48 @@
+
+variable sigma equal 3.405
+variable epsilon equal 0.238
+variable U0 equal 2*${epsilon}
+variable dlt equal 0.5
+variable x0 equal 5.0
+
+units real
+atom_style atomic
+pair_style lj/cut 3.822
+pair_modify shift yes
+boundary p p p
+
+region myreg block −25 25 −5 5 −25 25
+create_box 1 myreg
+create_atoms 1 random 200 34134 myreg overlap 1.5 maxtry 50
+
+mass * 39.95
+pair_coeff * * ${epsilon} ${sigma}
+neigh_modify every 1 delay 4 check yes
+
+minimize 1e−4 1e−6 100 1000
+reset_timestep 0
+
+variable U atom ${U0}*atan((x+${x0})/${dlt})-${U0}*atan((x−${x0})/${dlt})
+variable F atom ${U0}/((x−${x0})^2/${dlt}^2+1)/${dlt}-${U0}/((x+${x0})^2/${dlt}^2+1)/${dlt}
+fix myadf all addforce v_F 0.0 0.0 energy v_U
+
+fix mynve all nve
+fix mylgv all langevin 119.8 119.8 50 1530917
+
+region mymes block −${x0} ${x0} INF INF INF INF
+variable n_center equal count(all,mymes)
+thermo_style custom step temp etotal v_n_center
+thermo 10000
+
+dump viz all image 50000 myimage−*.ppm type type &
+    shiny 0.1 box yes 0.01 view 180 90 zoom 7 size 1600 400
+dump_modify viz backcolor white acolor 1 cyan adiam 1 1 boxcolor black
+
+timestep 2.0
+run 500000
+reset_timestep 0
+
+compute cc1 all chunk/atom bin/1d x 0.0 1.0
+fix myac all ave/chunk 10 400000 4000000 cc1 density/number file density_profile.dat
+
+run 4000000

journal-article.bib

@@ -757,3 +757,14 @@ @article{della1992molecular
   year={1992},
   publisher={American Institute of Physics}
 }
+
+@article{loche2022molecular,
+  title={Molecular dynamics simulations of the evaporation of hydrated ions from aqueous solution},
+  author={Loche, Philip and Bonthuis, Douwe J and Netz, Roland R},
+  journal={Communications Chemistry},
+  volume={5},
+  number={1},
+  pages={55},
+  year={2022},
+  publisher={Nature Publishing Group UK London}
+}

lammps-tutorials.tex

@@ -3540,30 +3540,30 @@ \subsection{Tutorial 7: Free energy calculation}
 \end{figure}
 
 \noindent The objective of this tutorial is to measure the free energy profile
-of particles across a barrier potential using two methods: free sampling and
+of particles through a barrier potential using two methods: free sampling and
 umbrella sampling \cite{kastner2011umbrella, allen2017computer, frenkel2023understanding} (Fig.\,\ref{fig:US}).
-For simplicity and to reduce computation time, the barrier potential will be
-imposed on the atoms with an additional force, mimicking the presence of a repulsive
-area in the middle of the simulation box without the need to simulate extra atoms.
+To simplify the process and minimize computation time, the barrier potential will be
+imposed on the atoms using an additional force, mimicking the presence of a repulsive
+area in the middle of the simulation box without needing to simulate additional atoms.
 The procedure is valid for more complex systems and can be adapted to many other
-situations, such as measuring the adsorption barrier near an interface, or for
-calculating a translocation barrier through a membrane
-\cite{wilson1997adsorption, makarov2009computer, gravelle2021adsorption}.
+situations, such as measuring adsorption barriers near an interface or calculating
+translocation barriers through a membrane
+\cite{wilson1997adsorption, makarov2009computer, gravelle2021adsorption, loche2022molecular}.
 
 \subsubsection{Method 1: Free sampling}
 The most direct way to calculate a free energy profile is to extract the partition
 function from a classical (i.e.~unbiased) molecular dynamics simulation, and
-then estimate the Gibbs free energy using
+then estimate the Gibbs free energy by using
 \begin{equation}
 \Delta G = -RT \ln(p/p_0),
 \label{eq:G}
 \end{equation}
 where $\Delta G$ is the free energy difference, $R$ is the gas constant, $T$
 is the temperature, $p$ is the pressure, and $p_0$ is a reference pressure.
-As an illustration, let us apply this method to an extremely simple configuration
+As an illustration, let us apply this method to a simple configuration
 that consists of a few particles diffusing in a box in the presence of a
-position-dependent repelling force that makes the center of the box a relatively
-unfavorable area to explore.
+position-dependent repulsive force that makes the center of the box a less
+favorable area to explore.
 
 \paragraph{Basic LAMMPS parameters}
 \noindent Create a folder called \textit{FreeSampling/}, and create an input