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lammps-tutorials.tex

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@@ -1819,8 +1819,8 @@ \subsubsection{Preparing the water reservoir}
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kspace_style ewald 1e-5
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special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 1.0 angle yes
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\end{lstlisting}
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With the unit style \lmpcmd{real}, masses are in g/mole, distances in Å,
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time in fs, and energies in kcal/mole. With the \lmpcmd{atom\_style
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With the unit style \lmpcmd{real}, masses are in g/mol, distances in Å,
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time in fs, and energies in kcal/mol. With the \lmpcmd{atom\_style
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full}, each atom is a dot with a mass and a charge that can be linked
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by bonds, angles, dihedrals, and/or impropers. The
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\lmpcmd{bond\_style}, \lmpcmd{angle\_style}, and
@@ -2403,7 +2403,7 @@ \subsubsection{System preparation}
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mass Cl- 35.453
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mass WALL 26.9815
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\end{lstlisting}
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Each \lmpcmd{mass} command assigns a mass in grams/mole to an atom type.
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Each \lmpcmd{mass} command assigns a mass in g/mol to an atom type.
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The \flecmd{parameters.inc} file also contains the pair coefficients:
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\begin{lstlisting}
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pair_coeff O O 0.185199 3.1589
@@ -2414,7 +2414,7 @@ \subsubsection{System preparation}
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pair_coeff O WALL 0.4 2.86645
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\end{lstlisting}
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Each \lmpcmd{pair\_coeff} assigns the depth of the LJ potential (in
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kcal/mole), and the distance (in Ångströms) at which the
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kcal/mol), and the distance (in Ångströms) at which the
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particle-particle potential energy is 0. As noted in previous
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tutorials, with the important exception of \lmpcmd{pair\_coeff O WALL},
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pairwise interactions were only assigned between atoms of identical
@@ -4038,7 +4038,7 @@ \subsubsection{Method 2: Umbrella sampling}
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To generate the free energy profile from the particle positions saved in
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the \flecmd{umbrella-sampling.i.dat} files, we use the
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WHAM~\cite{kumar1992weighted,kumar1995multidim} algorithm as implemented
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by Marc Grossfield~\cite{grossfieldimplementation}. You can download it
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by Alan Grossfield~\cite{grossfieldimplementation}. You can download it
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from \href{http://membrane.urmc.rochester.edu/?page_id=126}{Alan
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Grossfield}'s website. Make sure you download the WHAM code version
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2.1.0 or later which introduces the \lmpcmd{units} command-line option

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