other algorithms for special purpose dynamics are described after
this.
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
-%In the final \secref{par} of this chapter a few principles are
-%given on which parallelization of {\gromacs} is based. The
-%parallelization is hardly visible for the user and is therefore not
-%treated in detail.
-%} % Brace matches ifthenelse test for gmxlite
-
A few issues are of general interest. In all cases the {\em system}
must be defined, consisting of molecules. Molecules again consist of
particles with defined interaction functions. The detailed
other aspects of the algorithm, such as pair list generation, update of
velocities and positions, coupling to external temperature and
pressure, conservation of constraints.
-\ifthenelse{\equal{\gmxlite}{1}}{}{
The {\em analysis} of the data generated by an MD simulation is treated in \chref{analysis}.
-} % Brace matches ifthenelse test for gmxlite
\section{Periodic boundary conditions\index{periodic boundary conditions}}
\label{sec:pbc}
Restriction (\ref{eqn:gridrc}) ensures that only 26 images need to be
considered.
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{The group concept}
\label{sec:groupconcept}\index{group}
The {\gromacs} MD and analysis programs use user-defined {\em groups} of
sparingly.
All non-bonded interactions between pairs of energy-monitor groups can
-be excluded\index{exclusions}
-\ifthenelse{\equal{\gmxlite}{1}}
-{.}
-{(see details in the User Guide).}
+be excluded\index{exclusions} (see details in the User Guide).
Pairs of particles from excluded pairs of energy-monitor groups
are not put into the pair list.
This can result in a significant speedup
\end{description}
The use of groups in {\gromacs} tools is described in
\secref{usinggroups}.
-%} % Brace matches ifthenelse test for gmxlite
\section{Molecular Dynamics}
\label{sec:MD}
\subsubsection{Topology and force field}
The system topology, including a description of the force field, must
be read in.
-\ifthenelse{\equal{\gmxlite}{1}}
-{.}
-{Force fields and topologies are described in \chref{ff}
-and \ref{ch:top}, respectively.}
+Force fields and topologies are described in \chref{ff}
+and \ref{ch:top}, respectively.
All this information is static; it is never modified during the run.
\subsubsection{Coordinates and velocities}
In the group scheme, a neighbor list is generated consisting of pairs
of groups of at least one particle. These groups were originally
-\swapindex{charge}{group}s \ifthenelse{\equal{\gmxlite}{1}}{}{(see
- \secref{chargegroup})}, but with a proper treatment of long-range
+\swapindex{charge}{group}s (see
+ \secref{chargegroup}), but with a proper treatment of long-range
electrostatics, performance in unbuffered simulations is their only advantage. A pair of groups
is put into the neighbor list when their center of geometry is within
the cut-off distance. Interactions between all particle pairs (one from
in the interaction kernel. This procedure is applied automatically,
unless the user set the pair-list buffer size manually.
-\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Energy drift and pair-list buffering}
For a canonical (NVT) ensemble, the average energy error caused by
diffusion of $j$ particles from outside the pair-list cut-off
\secref{mod_nb_int}). One then has a buffer with the size equal to the
neighbor list cut-off less the longest interaction cut-off.
-} % Brace matches ifthenelse test for gmxlite
\subsubsection{Simple search\swapindexquiet{simple}{search}}
Due to \eqnsref{box_rot}{simplerc}, the vector $\rvij$
many shifts of combinations of box vectors need to be considered to find
the nearest image.
-\ifthenelse{\equal{\gmxlite}{1}}{}{
\begin{figure}
\centerline{\includegraphics[width=8cm]{plots/nstric}}
grid search is equally fast for rectangular and triclinic boxes. Thus
for most protein and peptide simulations the rhombic dodecahedron will
be the preferred box shape.
-} % Brace matches ifthenelse test for gmxlite
-\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Charge groups}
\label{sec:chargegroup}\swapindexquiet{charge}{group}%
Charge groups were originally introduced to reduce cut-off artifacts
With the Verlet cut-off scheme, charge groups are ignored.
-} % Brace matches ifthenelse test for gmxlite
\subsection{Compute forces}
\label{subsec:forces}
\label{eqn:Xi}
\eeq
-\ifthenelse{\equal{\gmxlite}{1}}{}{
The {\gromacs} implementation of the virial computation is described
in \secref{virial}.
-} % Brace matches ifthenelse test for gmxlite
-
\subsection{The \swapindex{leap-frog}{integrator}}
\label{subsec:update}
to the larger one. This not only halves the number of force calculations,
but also the update calculations. For even larger time steps, angle vibrations
involving hydrogen atoms can be removed using virtual interaction
-\ifthenelse{\equal{\gmxlite}{1}}
-{sites,}
-{sites (see \secref{rmfast}),}
+sites (see \secref{rmfast}),
which brings the shortest time step up to
PME mesh update frequency of a multiple time stepping scheme.
should therefore generally not be used when examining kinetics or
transport properties of the system.~\cite{Basconi2013}
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Nos{\'e}-Hoover temperature coupling\index{Nose-Hoover temperature coupling@Nos{\'e}-Hoover temperature coupling|see{temperature coupling, Nos{\'e}-Hoover}}{\index{temperature coupling Nose-Hoover@temperature coupling Nos{\'e}-Hoover}}\index{extended ensemble}}
The Berendsen weak-coupling algorithm is
and then using some algebra tricks to solve for some quantities are
required before they are actually calculated~\cite{Holian95}.
-% }
\subsubsection{Group temperature coupling}\index{temperature-coupling group}%
In {\gromacs} temperature coupling can be performed on groups of
ensemble, and it is not yet clear exactly what errors this approximation
may yield.
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Parrinello-Rahman pressure coupling\pawsindexquiet{Parrinello-Rahman}{pressure coupling}}
In cases where the fluctuations in pressure or volume are important
where the box volume integration occurs every step, but the auxiliary variable
integrations happen every $n$ steps.
-% } % Brace matches ifthenelse test for gmxlite
\subsection{The complete update algorithm}
the User Guide for details on how to set up your {\tt .mdp} file
to have {\tt mdrun} use this feature.
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Shell molecular dynamics}
{\gromacs} can simulate \normindex{polarizability} using the
\normindex{shell model} of Dick and Overhauser~\cite{Dick58}. In such models
\begin{equation}
\ve{x}_S(n+1) ~=~ \ve{x}_S(n) + \ve{F}_S/k_b.
\end{equation}
-% } % Brace matches ifthenelse test for gmxlite
\section{Constraint algorithms\index{constraint algorithms}}
Constraints can be imposed in {\gromacs} using LINCS (default) or
Lagrange multipliers (and hence the displacements) requires the
solution of a set of coupled equations of the second degree. These are
solved iteratively by SHAKE.
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\label{subsec:SETTLE}
For the special case of rigid water molecules, that often make up more
than 80\% of the simulation system we have implemented the
This step is called RATTLE, and is covered in more detail in the
original Andersen paper~\cite{Andersen1983a}.
-% } % Brace matches ifthenelse test for gmxlite
\newcommand{\con}{\ve{g}}
\newcommand{\lenc}{\ve{d}}
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{\normindex{LINCS}}
\label{subsec:lincs}
rotates over more than a predefined angle.
This angle is set by the user in the {\tt *.mdp} file.
-% } % Brace matches ifthenelse test for gmxlite
\section{Simulated Annealing}
\newcommand{\rond}{\stackrel{\circ}{r}}
\newcommand{\ruis}{\ve{r}^G}
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Stochastic Dynamics\swapindexquiet{stochastic}{dynamics}}
\label{sec:SD}
Stochastic or velocity \swapindex{Langevin}{dynamics} adds a friction
can be used. LINCS should be used for the constraints since SHAKE
will not converge for large atomic displacements.
BD is an option of the {\tt mdrun} program.
-% } % Brace matches ifthenelse test for gmxlite
\section{Energy Minimization}
\label{sec:EM}\index{energy minimization}%
$f=7.7$ kJ~mol$^{-1}$~nm$^{-1}$. A value for $\epsilon$ between 1 and
10 is acceptable.
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{Conjugate Gradient\index{conjugate gradient}}
Conjugate gradient is slower than steepest descent in the early stages
of the minimization, but becomes more efficient closer to the energy
gradient is only required for minimization prior to a normal-mode
analysis, which cannot be performed with constraints. For most other
purposes steepest descent is efficient enough.
-% } % Brace matches ifthenelse test for gmxlite
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{\normindex{L-BFGS}}
The original BFGS algorithm works by successively creating better
approximations of the inverse Hessian matrix, and moving the system to
improve the convergence, since sharp cut-offs mean the potential
function at the current coordinates is slightly different from the
previous steps used to build the inverse Hessian approximation.
-% } % Brace matches ifthenelse test for gmxlite
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Normal-Mode Analysis\index{normal-mode analysis}\index{NMA}}
Normal-mode analysis~\cite{Levitt83,Go83,BBrooks83b}
can be performed using {\gromacs}, by diagonalization of the mass-weighted
normal modes can be generated with {\tt \normindex{gmx nmens}}.
An overview of normal-mode analysis and the related principal component
analysis (see \secref{covanal}) can be found in~\cite{Hayward95b}.
-% } % Brace matches ifthenelse test for gmxlite
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Free energy calculations\index{free energy calculations}}
\label{sec:fecalc}
The $\lambda$-dependence for the force-field contributions is
described in detail in section \secref{feia}.
-% } % Brace matches ifthenelse test for gmxlite
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Replica exchange\index{replica exchange}}
Replica exchange molecular dynamics (\normindex{REMD})
is a method that can be used to speed up
separate rank. See the manual page of {\tt mdrun} on how to use these
multinode features.
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Essential Dynamics sampling\index{essential dynamics}\index{principal component analysis}\seeindexquiet{PCA}{covariance analysis}}
The results from Essential Dynamics (see \secref{covanal})
see {\tt gmx make_edi -h}.
The generated {\tt edi} input file is then passed to {\tt mdrun}.
-% } % Brace matches ifthenelse test for gmxlite
-% \ifthenelse{\equal{\gmxlite}{1}}{}{
\section{\normindex{Expanded Ensemble}}
In an expanded ensemble simulation~\cite{Lyubartsev1992}, both the coordinates and the
non-dimensional units, but they can be set to arbitrary values as
desired. Several different algorithms can be used to equilibrate
these weights, described in the mdp option listings.
-% } % Brace matches ifthenelse test for gmxlite
In {\gromacs}, this space is sampled by alternating sampling in the $k$
and $\vec{x}$ directions. Sampling in the $\vec{x}$ direction is done
Therefore a parallel constraint algorithm is required.
{\gromacs} uses the \normindex{P-LINCS} algorithm~\cite{Hess2008a},
which is the parallel version of the \normindex{LINCS} algorithm~\cite{Hess97}
-% \ifthenelse{\equal{\gmxlite}{1}}
-{.}
-{(see \ssecref{lincs}).}
+(see \ssecref{lincs}).
The P-LINCS procedure is illustrated in \figref{plincs}.
When molecules cross the cell boundaries, atoms in such molecules
up to ({\tt lincs_order + 1}) bonds away are communicated over the cell boundaries.
Electrostatics interactions are long-range, therefore special
algorithms are used to avoid summation over many atom pairs.
In {\gromacs} this is usually
-% \ifthenelse{\equal{\gmxlite}{1}}
-{.}
-{PME (\secref{pme}).}
+PME (\secref{pme}).
Since with PME all particles interact with each other, global communication
is required. This will usually be the limiting factor for
scaling with domain decomposition.
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
C-terminus and hydrogens on the N-terminus
\item[{\tt SideChain-H}]\mbox{}\\
protein side chain atoms excluding all hydrogens
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\item[{\tt Prot-Masses}]\mbox{}\\
protein atoms excluding dummy masses (as used in virtual site
constructions of NH$_3$ groups and tryptophan side-chains),
see also \secref{vsitetop}; this group is only included when
it differs from the ``{\tt Protein}'' group
-%} % Brace matches ifthenelse test for gmxlite
\item[{\tt Non-Protein}]\mbox{}\\
all non-protein atoms
\item[{\tt DNA}]\mbox{}\\
up to $r_{max}$, so angle dependent, see \figref{rdfex}D.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Correlation functions
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Correlation functions}
\label{sec:corr}
{\tt \normindex{gmx energy}} can compute the viscosity,
but this is not very accurate~\cite{Hess2002a}, and
actually the values do not converge.
-%} % Brace matches ifthenelse test for gmxlite
\section{Curve fitting in \gromacs}
\subsection{Sum of exponential functions}
\label{fig:msdwater}
\end{figure}
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
%
%%%%%%%%%%%%%%%%%%%%% Bonds, angles and dihedral %%%%%%%%%%%%%%%%%%%
%
interchangeably.}
\label{fig:sgangle}
\end{figure}
-%} % Brace matches ifthenelse test for gmxlite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Radius of gyration and distances
\item[$\bullet$]
The {\em distance between the geometrical centers} of two groups can be
calculated with the program
-%\ifthenelse{\equal{\gmxlite}{1}}{
{{\tt \normindex{gmx distance}}, as explained in \secref{bad}.}
\item[$\bullet$]
The {\em minimum distance} between two groups of atoms during time
where the {\em distance} {\bf r}$_{ij}$ between atoms at time $t$
is compared with the distance between the same atoms at time $0$.
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Covariance analysis\index{covariance analysis}}
\label{sec:covanal}
Covariance analysis, also called
The principal components and overlap (and many more things)
can be plotted and analyzed with {\tt \normindex{gmx anaeig}}.
The cosine content can be calculated with {\tt \normindex{gmx analyze}}.
-%} % Brace matches ifthenelse test for gmxlite
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Dihedral principal component analysis}
{\tt gmx angle, gmx covar, gmx anaeig}\\
Principal component analysis can be performed in dihedral
gmx covar} since the coordinates in the dummy reference file do not
correspond in any way to the information in the {\tt .trr} file. Analysis of
the results is done using {\tt gmx anaeig}.
-%} % Brace matches ifthenelse test for gmxlite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Hydrogen bonds
\end{itemize}
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Protein related items
% to be more up-to-date.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%} % Brace matches ifthenelse test for gmxlite
% LocalWords: Xmgr ndx mk angndx rdf dihedrals grompp hydrogens MainChain Prot
% LocalWords: oxygens SideChain tryptophan vsitetop aminoacids dat ngmx dr SPC
\item {\em Restraints}: position restraints, angle restraints,
distance restraints, orientation restraints and dihedral restraints, all
based on fixed lists.
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\item {\em Applied Forces}:
externally applied forces, see \chref{special}.
-%}
\end{enumerate}
\section{Non-bonded interactions}
This last rule is used by the OPLS force field.
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{\normindex{Buckingham potential}}
The Buckingham
potential has a more flexible and realistic repulsion term
6\frac{C_{ij}}{\rij^7} \right] \rnorm
\eeq
-%} % Brace matches ifthenelse test for gmxlite
\subsection{Coulomb interaction}
\label{sec:coul}
\normindex{$\epsr$}
may be set in the in the input for {\tt grompp}.
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{Coulomb interaction with \normindex{reaction field}}
\label{sec:coulrf}
The Coulomb interaction can be modified for homogeneous systems by
between the direct space sum and the reciprocal space sum and erfc$(x)$ is
the complementary error function. For further
details on long-range electrostatics, see \secref{lr_elstat}.
-%} % Brace matches ifthenelse test for gmxlite
\section{Bonded interactions}
\ve{F}_i(\rvij) = k^b_{ij}(\rij-b_{ij}) \rnorm
\eeq
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Fourth power potential}
\label{subsec:G96bond}
In the \gromosv{96} force field~\cite{gromos96}, the covalent bond potential
\eeq
At short distances the potential asymptotically goes to a harmonic
potential with force constant $k^b$, while it diverges at distance $b$.
-%} % Brace matches ifthenelse test for gmxlite
\subsection{Harmonic angle potential}
\label{subsec:harmonicangle}
{\bf Note} that in the input in topology files, angles are given in degrees and
force constants in kJ/mol/rad$^2$.
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{Cosine based angle potential}
\label{subsec:G96angle}
In the \gromosv{96} force field a simplified function is used to represent angle
\beq
V_q(\tijk) ~=~ \sum_{n=0}^5 C_n (\tijk-\tijk^0)^n
\eeq
-%} % Brace matches ifthenelse test for gmxlite
%% new commands %%%%%%%%%%%%%%%%%%%%%%
\newcommand{\rvkj}{{\bf r}_{kj}}
V_d(\phi_{ijkl}) = k_{\phi}(1 + \cos(n \phi - \phi_s))
\eeq
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Proper dihedrals: Ryckaert-Bellemans function}
\label{subsec:RBdihedral}
For alkanes, the following proper dihedral potential is often used
cos$(\phi)$).\\
\noindent{\bf Note:} Mind the conversion from {\bf kcal mol$^{-1}$} for
literature OPLS and RB parameters to {\bf kJ mol$^{-1}$} in {\gromacs}.\\
-%} % Brace matches ifthenelse test for gmxlite
\subsubsection{Proper dihedrals: Fourier function}
\label{subsec:Fourierdihedral}
V_{F} (\phi_{ijkl}) ~=~ \frac{1}{2} \left[C_1(1+\cos(\phi)) + C_2(
1-\cos(2\phi)) + C_3(1+\cos(3\phi)) + C_4(1-\cos(4\phi))\right],
\eeq
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
Internally, {\gromacs}
uses the Ryckaert-Bellemans code
to compute Fourier dihedrals (see above), because this is more efficient.\\
(due to the cancelling of the torsion potential) but the next step would be singular
($\theta$ is not $180^{\circ}$ and $\phi$ is very close to $180^{\circ}$).
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{Tabulated bonded interaction functions\index{tabulated bonded interaction function}}
\label{subsec:tabulatedinteraction}
For full flexibility, any functional shape can be used for
-180 up to and including 180 degrees;
the IUPAC/IUB convention is used, {\ie} zero is cis,
the derivative is taken in degrees.
-%} % Brace matches ifthenelse test for gmxlite
\section{Restraints}
Special potentials are used for imposing restraints on the motion of
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{Angle restraints\swapindexquiet{angle}{restraint}}
\label{subsec:anglerestraint}
These are used to restrain the angle between two pairs of particles
constant.
{\bf Note} that in the input in topology files, angles are given in degrees and
force constants in kJ/mol/rad$^2$.
-%} % Brace matches ifthenelse test for gmxlite
\subsection{Distance restraints\swapindexquiet{distance}{restraint}}
\label{subsec:distancerestraint}
In {\gromacs} there are three ways to impose restraints on pairs of atoms:
\begin{itemize}
\item Simple harmonic restraints: use {\tt [ bonds ]} type 6
-%\ifthenelse{\equal{\gmxlite}{1}}
-{.}
-{(see \secref{excl}).}
+(see \secref{excl}).
\item\label{subsec:harmonicrestraint}Piecewise linear/harmonic restraints: {\tt [ bonds ]} type 10.
\item Complex NMR distance restraints, optionally with pair, time and/or
ensemble averaging.
For restraints not derived from NMR data, this functionality
will usually suffice and a section of {\tt [ bonds ]} type 10
can be used to apply individual restraints between pairs of
-%\ifthenelse{\equal{\gmxlite}{1}}{atoms.}{
atoms, see \ssecref{topfile}.
-%} % Brace matches ifthenelse test for gmxlite
For applying restraints derived from NMR measurements, more complex
functionality might be required, which is provided through
the {\tt [~distance_restraints~]} section and is described below.
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Time averaging\swapindexquiet{time-averaged}{distance restraint}}
Distance restraints based on instantaneous distances can potentially reduce
the fluctuations in a molecule significantly. This problem can be overcome by restraining
multiplied by the value in the column {\tt fac} for each restraint.
Information for each restraint is stored in the energy file and can
be processed and plotted with {\tt gmx nmr}.
-%} % Brace matches ifthenelse test for gmxlite
\newcommand{\SSS}{{\mathbf S}}
\newcommand{\DD}{{\mathbf D}}
\newcommand{\RR}{{\mathbf R}}
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsection{Orientation restraints\swapindexquiet{orientation}{restraint}}
\label{subsec:orientationrestraint}
This section describes how orientations between vectors,
force constants and averaging times and ensemble averaging see~\cite{Hess2003}.
Information for each restraint is stored in the energy file and can
be processed and plotted with {\tt gmx nmr}.
-%} % Brace matches ifthenelse test for gmxlite
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Polarization}
Polarization can be treated by {\gromacs} by attaching
\normindex{shell} (\normindex{Drude}) particles to atoms and/or
2.6~\cite{Noskov2005a}; $\alpha_i$ and $\alpha_j$ are the polarizabilities
of the respective shell particles.
-%} % Brace matches ifthenelse test for gmxlite
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Free energy interactions}
\label{sec:feia}
\index{free energy interactions}
should satisfy $0.001 < \alpha < 0.003$, rather than $\alpha \approx
0.5$.
-%} % Brace matches ifthenelse test for gmxlite
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Methods}
\subsection{Exclusions and 1-4 Interactions.}
Atoms within a molecule that are close by in the chain,
forms of the non-bonded interactions.}
\label{tab:funcparm}
\end{table}
-%} % Brace matches ifthenelse test for gmxlite
\newcommand{\vvis}{\ve{r}_s}
\newcommand{\rvjk}{\ve{r}_{jk}}
\newcommand{\rvjl}{\ve{r}_{jl}}
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
+
\section{Virtual interaction sites\index{virtual interaction sites}}
\label{sec:virtual_sites}
Virtual interaction sites (called \seeindex{dummy atoms}{virtual interaction sites} in {\gromacs} versions before 3.3)
\end{itemize}
\end{itemize}
-%} % Brace matches ifthenelse test for gmxlite
\newcommand{\dr}{{\rm d}r}
\newcommand{\avcsix}{\left< C_6 \right>}
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Long Range Electrostatics}
\label{sec:lr_elstat}
\subsection{Ewald summation\index{Ewald sum}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Long Range Van der Waals interactions}
\subsection{Dispersion correction\index{dispersion correction}}
In this section, we derive long-range corrections due to the use of a
PME-only ranks, more such ranks should be used. It may be possible to
improve upon the automatic load-balancing used by {\tt mdrun}.
-%} % Brace matches ifthenelse test for gmxlite
\section{Force field\index{force field}}
\label{sec:ff}
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
Keywords={GROMACS; molecular dynamics; molecular simulation; free energy; SIMD; GPU; GPGPU; MPI; OpenMP}
}}
-% If you set gmxlite to 1 a very much shortened version of the manual
-% will be generated, which may be useful for teaching.
-\newcommand{\gmxlite}{0}
-
\begin{document}
%roman pagenumbers for the preamble stuff
\includegraphics[height=5in]{plots/peregrine}
\vspace{4mm}
-\ifthenelse{\equal{\gmxlite}{1}}
-{
-\fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont Reference Manual {\em ~Lite~}}}
-}
-{
\fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont ~Reference Manual~}}
-} % Brace matches ifthenelse test for gmxlite
\vspace{4mm}
\textcolor{blue}{\fontsize{48}{56} \selectfont ~Version \gmxver~}
\end{center}
\vfill
-\ifthenelse{\equal{\gmxlite}{1}}
-{
-\newpage
-{\bf
-This text is a shortened version of the full {\gromacs} manual, written
-by David van der Spoel, Berk Hess, Erik Lindahl and others. Please
-find further information on our website {\wwwpage}.}
-
-\vspace{2cm}
-
-\noindent \copyright\ 1991--2000:
-Department of Biophysical Chemistry, University of Groningen.
-Nijenborgh 4, 9747 AG Groningen, The Netherlands.\\
-\medskip
-
-\noindent \copyright\ 2001--{\gmxyear}:
-The {\gromacs} development teams at the Royal Institute of Technology and \\
-Uppsala University, Sweden.
-}
-{
\cleardoublepage
-} % Brace matches ifthenelse test for gmxlite
%reset to normal margins
\addtolength{\oddsidemargin}{5mm}
\rhead[\fancyplain{}{\em\leftmark}]{\fancyplain{}{\em\thepage}}
\cfoot{}
-\ifthenelse{\equal{\gmxlite}{1}}{}{
\begin{center}
\phantom{ }
\vspace{1cm}
The {\gromacs} source code and and selected set of binary packages are
available on our homepage, \wwwpage. Have fun.
-} % Brace matches ifthenelse test for gmxlite
\newpage
% C O N T E N T S
\include{algorithms}
\include{forcefield}
-\ifthenelse{\equal{\gmxlite}{1}}{}{
\include{topology}
\include{special}
\include{programs}
-} % Brace matches ifthenelse test for gmxlite
\include{analyse}
-\ifthenelse{\equal{\gmxlite}{1}}{}{
%
% A P P E N D I C E S
%
\include{technical}
\include{implement}
\include{averages}
-} % Brace matches ifthenelse test for gmxlite
%
% The pdfdummy counter is a workaround to get correct
% bookmarks for the index & bibliography in pdf files
\cleardoublepage
\refstepcounter{pdfdummy}
-\ifthenelse{\equal{\gmxlite}{1}}{}{
\addcontentsline{toc}{chapter}{Index}
\renewcommand{\see}[2]{\mbox{} \mbox{\textit{see} #1}}
\printindex
-} % Brace matches ifthenelse test for gmxlite
\end{document}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff