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} \\
\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{$\epsr$}
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.
\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}
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
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
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,
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,
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
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
\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.
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}
\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})
;
; Example topology file
;
-; The force field files to be included
+; The force-field files to be included
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
{\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
{\small
\begin{verbatim}
-; Include force field parameters
+; Include force-field parameters
#include "gromos43a1.ff/forcefield.itp"
[ moleculetype ]
\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 <name>.ff} directories
A force field is included at the beginning of a topology file with an
{\tt \#include} statement followed by {\tt <name>.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}.
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
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.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff