From 2cf6ccda1d58348be3cd34f91b08a0ed2d1c8f5d Mon Sep 17 00:00:00 2001 From: Rossen Apostolov Date: Thu, 19 Jun 2014 11:48:16 +0200 Subject: [PATCH] Use cosistent style when referring to force fields. Refs #677. Change-Id: I386c6d9782c88d5af929a3230cd3beb06f2cfbd2 --- manual/forcefield.tex | 8 ++++---- manual/install.tex | 2 +- manual/special.tex | 6 +++--- manual/topology.tex | 32 ++++++++++++++++---------------- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/manual/forcefield.tex b/manual/forcefield.tex index d99292b8c8..1b7167ecf0 100644 --- a/manual/forcefield.tex +++ b/manual/forcefield.tex @@ -102,7 +102,7 @@ V_{LJ}(\rvij) = 4\epsilon_{ij}\left(\left(\frac{\sigma_{ij}} {\rij}\right)^{12} In constructing the parameter matrix for the non-bonded LJ-parameters, two types of \normindex{combination rule}s can be used within {\gromacs}, -only geometric averages (type 1 in the input section of the force field file): +only geometric averages (type 1 in the input section of the force-field file): \beq \begin{array}{rcl} C_{ij}^{(6)} &=& \left({C_{ii}^{(6)} \, C_{jj}^{(6)}}\right)^{1/2} \\ @@ -178,7 +178,7 @@ The force derived from this potential is: \ve{F}_i(\rvij) = f \frac{q_i q_j}{\epsr\rij^2}\rnorm \eeq -A plain Coulomb interaction should only be used without cut-off or when all pairs fall within the cut-off, since there is an abrupt, large change in the force at the cut-off. In case you do want to use a cut-off, the potential can be shifted by a constant to make the potential the integral of the force. With the group cut-off scheme, this shift is only applied to non-excluded pairs. With the Verlet cut-off scheme, the shift is also applied to excluded pairs and self interactions, which makes the potential equivalent to a reaction-field with $\epsrf=1$ (see below). +A plain Coulomb interaction should only be used without cut-off or when all pairs fall within the cut-off, since there is an abrupt, large change in the force at the cut-off. In case you do want to use a cut-off, the potential can be shifted by a constant to make the potential the integral of the force. With the group cut-off scheme, this shift is only applied to non-excluded pairs. With the Verlet cut-off scheme, the shift is also applied to excluded pairs and self interactions, which makes the potential equivalent to a reaction field with $\epsrf=1$ (see below). In {\gromacs} the relative \swapindex{dielectric}{constant} \normindex{$\epsr$} @@ -2877,7 +2877,7 @@ When selecting the CHARMM force field in {\tt \normindex{pdb2gmx}} the default o A port of the CHARMM36 force field for use with GROMACS is also available at \url{http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs}. -\subsection{Coarse-grained force-fields} +\subsection{Coarse-grained force fields} \index{force-field, coarse-grained} \label{sec:cg-forcefields} Coarse-graining is a systematic way of reducing the number of degrees of freedom representing a system of interest. To achieve this, typically whole groups of atoms are represented by single beads and the coarse-grained force fields describes their effective interactions. Depending on the choice of parameterization, the functional form of such an interaction can be complicated and often tabulated potentials are used. @@ -2887,7 +2887,7 @@ Coarse-grained models are designed to reproduce certain properties of a referenc \item Conserving free energies \begin{itemize} \item Simplex method -\item MARTINI force-field (see next section) +\item MARTINI force field (see next section) \end{itemize} \item Conserving distributions (like the radial distribution function), so-called structure-based coarse-graining \begin{itemize} diff --git a/manual/install.tex b/manual/install.tex index 8c51ddbc79..5cc9245aa8 100644 --- a/manual/install.tex +++ b/manual/install.tex @@ -104,7 +104,7 @@ In most cases this is not really a problem, since the fluctuations in the virial can be two orders of magnitude larger than the average. Using cut-offs for the Coulomb interactions cause large errors in the energies, forces, and virial. -Even when using a reaction-field or lattice sum method, the errors +Even when using a reaction-field or lattice-sum method, the errors are larger than, or comparable to, the errors due to the single precision. Since MD is chaotic, trajectories with very similar starting conditions will diverge rapidly, the divergence is faster in single precision than in double diff --git a/manual/special.tex b/manual/special.tex index 7901c69585..f2514cea1c 100644 --- a/manual/special.tex +++ b/manual/special.tex @@ -1256,7 +1256,7 @@ virtualized as well, {\ie} hydrogens in the aromatic residues are treated differently depending on the treatment of the aromatic residues. Parameters for the virtual site constructions for the hydrogen atoms are -inferred from the force field parameters ({\em vis}. bond lengths and +inferred from the force-field parameters ({\em vis}. bond lengths and angles) directly by {\tt \normindex{grompp}} while processing the topology file. The constructions for the aromatic residues are based on the bond lengths and angles for the geometry as described in the @@ -1678,7 +1678,7 @@ double sums is the total electrostatic interaction between the QM electrons and the MM atoms. The total electrostatic interaction of the QM nuclei with the MM atoms is given by the second double sum. Bonded interactions between QM and MM atoms are described at the MM level by -the appropriate force field terms. Chemical bonds that connect the two +the appropriate force-field terms. Chemical bonds that connect the two subsystems are capped by a hydrogen atom to complete the valence of the QM region. The force on this atom, which is present in the QM region only, is distributed over the two atoms of the bond. The cap @@ -1719,7 +1719,7 @@ To make use of the QM/MM functionality in {\gromacs}, one needs to: At the bond that connects the QM and MM subsystems, a link atoms is introduced. In {\gromacs} the link atom has special atomtype, called LA. This atomtype is treated as a hydrogen atom in the QM calculation, -and as a virtual site in the force field calculation. The link atoms, if +and as a virtual site in the force-field calculation. The link atoms, if any, are part of the system, but have no interaction with any other atom, except that the QM force working on it is distributed over the two atoms of the bond. In the topology, the link atom (LA), therefore, diff --git a/manual/topology.tex b/manual/topology.tex index 87782be2f7..9646061882 100644 --- a/manual/topology.tex +++ b/manual/topology.tex @@ -603,7 +603,7 @@ working directory, then in the {\gromacs} {\tt share/top} directory, and use the first matching {\tt xxx.ff} directory found. Two general files are read by {\tt pdb2gmx}: an atom type file -(extension {\tt .atp}, see~\ssecref{atomtype}) from the force field directory, +(extension {\tt .atp}, see~\ssecref{atomtype}) from the force-field directory, and a file called {\tt residuetypes.dat} from either the working directory, or the {\gromacs} {\tt share/top} directory. {\tt residuetypes.dat} determines which residue names are considered protein, DNA, RNA, @@ -725,7 +725,7 @@ the standard parameters in the {\tt .itp} files. This should only be used in special cases. Instead of parameters, a string can be added for each bonded interaction. This is used in \gromosv{96} {\tt .rtp} files. These strings are copied to the topology file and can be -replaced by force field parameters by the C-preprocessor in {\tt grompp} +replaced by force-field parameters by the C-preprocessor in {\tt grompp} using {\tt \#define} statements. {\tt pdb2gmx} automatically generates all angles. This means that for @@ -755,8 +755,8 @@ Each force field has its own naming convention for residues. Most residues have consistent naming, but some, especially those with different protonation states, can have many different names. The {\tt .r2b} files are used to convert standard residue names to -the force field build block names. If no {\tt .r2b} is present -in the force field directory or a residue is not listed, the building +the force-field build block names. If no {\tt .r2b} is present +in the force-field directory or a residue is not listed, the building block name is assumed to be identical to the residue name. The {\tt .r2b} can contain 2 or 5 columns. The 2-column format has the residue name in the first column and the building block name @@ -805,7 +805,7 @@ HEME & heme \\ \subsection{Atom renaming database} Force fields often use atom names that do not follow IUPAC or PDB convention. The {\tt .arn} database is used to translate the atom names in the coordinate -file to the force field names. Atoms that are not listed keep their names. +file to the force-field names. Atoms that are not listed keep their names. The file has three columns: the building block name, the old atom name, and the new atom name, respectively. The residue name supports question-mark wildcards that match a single character. @@ -813,9 +813,9 @@ supports question-mark wildcards that match a single character. An additional general atom renaming file called {\tt xlateat.dat} is present in the {\tt share/top} directory, which translates common non-standard atom names in the coordinate file to IUPAC/PDB convention. Thus, when writing -force field files, you can assume standard atom names and no further +force-field files, you can assume standard atom names and no further atom name translation is required, except for translating from standard atom names -to the force field ones. +to the force-field ones. \subsection{Hydrogen database} \label{subsec:hdb} @@ -1269,7 +1269,7 @@ Description of the file layout: \item Directives are surrounded by {\tt [} and {\tt ]} \item The topology hierarchy (which must be followed) consists of three levels: \begin{itemize} -\item the parameter level, which defines certain force field specifications +\item the parameter level, which defines certain force-field specifications (see~\tabref{topfile1}) \item the molecule level, which should contain one or more molecule definitions (see~\tabref{topfile2}) @@ -1315,7 +1315,7 @@ Here is an example of a topology file, {\tt urea.top}: ; ; Example topology file ; -; The force field files to be included +; The force-field files to be included #include "amber99.ff/forcefield.itp" [ moleculetype ] @@ -1769,7 +1769,7 @@ lambda is not equal to zero or one. {\bf Note} that this topology uses the \gromosv{96} force field, in which the bonded interactions are not determined by the atom types. The bonded interaction -strings are converted by the C-preprocessor. The force field parameter +strings are converted by the C-preprocessor. The force-field parameter files contain lines like: {\small @@ -1803,7 +1803,7 @@ each of the constraint components. This functionality is planned for later vers {\small \begin{verbatim} -; Include force field parameters +; Include force-field parameters #include "gromos43a1.ff/forcefield.itp" [ moleculetype ] @@ -1880,7 +1880,7 @@ tensor, not a vector. \section{Force field organization \index{force field organization}} \label{sec:fforganization} -\subsection{Force field files} +\subsection{Force-field files} \label{subsec:fffiles} Many force fields are available by default. Force fields are detected by the presence of {\tt .ff} directories @@ -1911,8 +1911,8 @@ The force fields included with {\gromacs} are: A force field is included at the beginning of a topology file with an {\tt \#include} statement followed by {\tt .ff/forcefield.itp}. -This statement includes the force field file, -which, in turn, may include other force field files. All the force fields +This statement includes the force-field file, +which, in turn, may include other force-field files. All the force fields are organized in the same way. An example of the {\tt amber99.ff/forcefield.itp} was shown in \ssecref{topfile}. @@ -1924,7 +1924,7 @@ the atom type database ({\tt .atp}, see~\ssecref{atomtype}), which contains only files are described in~\secref{pdb2gmxfiles}. -\subsection{Changing force field parameters\index{force field}} +\subsection{Changing force-field parameters\index{force field}} If one wants to change the parameters of few bonded interactions in a molecule, this is most easily accomplished by typing the parameters behind the definition of the bonded interaction directly in the {\tt *.top} file @@ -1951,7 +1951,7 @@ As of {\gromacs} version 3.1.3, atom types can be added in an extra force field. After the definition of the new atom type(s), additional non-bonded and pair parameters can be defined. In pre-3.1.3 versions of {\gromacs}, the new atom types needed to be -added in the {\tt [~atomtypes~]} section of the force field files, +added in the {\tt [~atomtypes~]} section of the force-field files, because all non-bonded parameters above the last {\tt [~atomtypes~]} section would be overwritten using the standard combination rules. -- 2.22.0