From efd495509bf859d229012c3a92b507ff99ead47e Mon Sep 17 00:00:00 2001 From: Paul Bauer Date: Mon, 30 Oct 2017 15:40:16 +0100 Subject: [PATCH] Small change to LaTeX manual generation Removed the gmxlite if statements in the pdf manual source files. They made it more difficult to generate the new markup style files and are apparently not needed. Change-Id: Ica401f103c8f9682c7a45bdd90aa8680db7ff56a --- docs/manual/algorithms.tex | 72 ++++++---------------------------------------- docs/manual/analyse.tex | 15 +--------- docs/manual/forcefield.tex | 39 ++----------------------- docs/manual/gromacs.tex | 41 +------------------------- 4 files changed, 12 insertions(+), 155 deletions(-) diff --git a/docs/manual/algorithms.tex b/docs/manual/algorithms.tex index b9b4206b1b..c51011a374 100644 --- a/docs/manual/algorithms.tex +++ b/docs/manual/algorithms.tex @@ -63,13 +63,6 @@ given, which is refined in subsequent subsections. The (simple) EM 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 @@ -79,9 +72,7 @@ field} and the calculation of forces is given in 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} @@ -255,7 +246,6 @@ translation with the indexed vector (see \ssecref{forces}). 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 @@ -308,10 +298,7 @@ that would lead to 256$\times$256 items! Better use this concept 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 @@ -337,7 +324,6 @@ specified, than all atoms are saved to the compressed trajectory file. \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} @@ -391,10 +377,8 @@ actual MD run check the online manual at {\wwwpage}. \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} @@ -500,8 +484,8 @@ cut-off schemes, please see the User Guide. 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 @@ -572,7 +556,6 @@ little overhead and significantly reduce the number of cluster pairs 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 @@ -757,7 +740,6 @@ list cut-off (there are several ways to do this in {\gromacs}, see \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 $\rvij$ @@ -773,7 +755,6 @@ that do not obey \eqnref{box_rot}, 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}} @@ -802,9 +783,7 @@ algorithm when there are more than a few hundred particles. The 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 @@ -842,7 +821,6 @@ are connected to; for example: CH$_3$, CH$_2$, CH, NH$_2$, NH, OH, CO$_2$, CO. With the Verlet cut-off scheme, charge groups are ignored. -} % Brace matches ifthenelse test for gmxlite \subsection{Compute forces} \label{subsec:forces} @@ -911,11 +889,8 @@ The virial ${\bf \Xi}$ tensor is defined as: \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} @@ -1120,9 +1095,7 @@ oscillator), which allows the smallest time step to be increased 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. @@ -1268,7 +1241,6 @@ $\tau_T$ is at moderate levels (less than 10 ps). This algorithm 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 @@ -1427,7 +1399,6 @@ Eq.~\ref{eq:half_step_NHC_integrator} just before the $\exp\left(iL_1 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 @@ -1542,7 +1513,6 @@ with the correct average pressure, it does not yield the exact NPT 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 @@ -1814,7 +1784,6 @@ For pressure control, this becomes 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} @@ -1901,7 +1870,6 @@ format. All the other tools can read and write this format. See 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 @@ -1948,7 +1916,6 @@ of shell positions \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 @@ -1993,7 +1960,6 @@ Verlet algorithm is equal to $(\ve{G}_i/m_i)(\Dt)^2$. Solving the 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 @@ -2006,7 +1972,6 @@ removing any component of the velocity parallel to the bond vector. This step is called RATTLE, and is covered in more detail in the original Andersen paper~\cite{Andersen1983a}. -% } % Brace matches ifthenelse test for gmxlite @@ -2023,7 +1988,6 @@ original Andersen paper~\cite{Andersen1983a}. \newcommand{\con}{\ve{g}} \newcommand{\lenc}{\ve{d}} -% \ifthenelse{\equal{\gmxlite}{1}}{}{ \subsection{\normindex{LINCS}} \label{subsec:lincs} @@ -2196,7 +2160,6 @@ However, LINCS will generate a warning when in one step a bond 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} @@ -2225,7 +2188,6 @@ match both types of annealing and non-annealed groups in your simulation. \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 @@ -2298,7 +2260,6 @@ Because the system is assumed to be over-damped, large timesteps 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}% @@ -2346,7 +2307,6 @@ $k$ Boltzmann's constant. For a weak oscillator with a wave number of $f=7.7$ 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 @@ -2361,9 +2321,7 @@ This is not really a restriction, since the accuracy of conjugate 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 @@ -2381,9 +2339,7 @@ It is also noteworthy that switched or shifted interactions usually 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 @@ -2433,9 +2389,7 @@ Ensembles of structures at any temperature and for any subset of 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} @@ -2581,9 +2535,7 @@ the external {\tt pymbar} package, at https://SimTK.org/home/pymbar. 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 @@ -2692,7 +2644,6 @@ parallelism in the algorithm. For efficiency each replica can run on a 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}) @@ -2723,9 +2674,7 @@ which has many options for selecting vectors and setting parameters, 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 @@ -2746,7 +2695,6 @@ probability, in which case $g_k$ is equal to the free energy in 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 @@ -2913,9 +2861,7 @@ on different ranks, bond constraints can cross cell boundaries. 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. @@ -3001,9 +2947,7 @@ one might want to set $r_{\mathrm{mb}}$ by hand to reduce this cost. 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. diff --git a/docs/manual/analyse.tex b/docs/manual/analyse.tex index ca3e5344a8..6f3cf1c46d 100644 --- a/docs/manual/analyse.tex +++ b/docs/manual/analyse.tex @@ -1,7 +1,7 @@ % % 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. @@ -136,13 +136,11 @@ a number of \swapindex{default}{groups} are generated to choose from: 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{}\\ @@ -339,7 +337,6 @@ the average density in all angle slices from $\theta$ to $\theta + d\theta$ up to $r_{max}$, so angle dependent, see \figref{rdfex}D. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Correlation functions -%\ifthenelse{\equal{\gmxlite}{1}}{}{ \section{Correlation functions} \label{sec:corr} @@ -478,7 +475,6 @@ time of the Pressure tensor $\ve{P}$~\cite{PSmith93c,Balasubramanian96}. {\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} @@ -621,7 +617,6 @@ An example of the mean square displacement of SPC water is given in \label{fig:msdwater} \end{figure} -%\ifthenelse{\equal{\gmxlite}{1}}{}{ % %%%%%%%%%%%%%%%%%%%%% Bonds, angles and dihedral %%%%%%%%%%%%%%%%%%% % @@ -711,7 +706,6 @@ Also other combinations are supported: planes and vectors can be used interchangeably.} \label{fig:sgangle} \end{figure} -%} % Brace matches ifthenelse test for gmxlite %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Radius of gyration and distances @@ -743,7 +737,6 @@ possibilities: \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 @@ -813,7 +806,6 @@ RMSD(t) ~=~ \left[\frac{1}{N^2}\sum_{i=1}^N \sum_{j=1}^N \|{\bf r}_{ij}(t 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 @@ -939,9 +931,7 @@ The covariance matrix is built and diagonalized by 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 @@ -963,7 +953,6 @@ You should use the {\tt -nofit} option for {\tt 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 @@ -1052,7 +1041,6 @@ the analyzed groups and all solvent atoms involved in insertion. \end{itemize} -%\ifthenelse{\equal{\gmxlite}{1}}{}{ % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Protein related items @@ -1180,7 +1168,6 @@ atoms across the interface. % 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 diff --git a/docs/manual/forcefield.tex b/docs/manual/forcefield.tex index ea969e8a51..8574bc4094 100644 --- a/docs/manual/forcefield.tex +++ b/docs/manual/forcefield.tex @@ -51,10 +51,8 @@ basis of fixed lists. \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} @@ -132,7 +130,6 @@ finally an geometric average for both parameters can be used (type 3): 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 @@ -154,7 +151,6 @@ See also \figref{bham}. The force derived from this is: 6\frac{C_{ij}}{\rij^7} \right] \rnorm \eeq -%} % Brace matches ifthenelse test for gmxlite \subsection{Coulomb interaction} \label{sec:coul} @@ -189,7 +185,6 @@ In {\gromacs} the relative \swapindex{dielectric}{constant} \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 @@ -373,7 +368,6 @@ where $\beta$ is a parameter that determines the relative weight 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} @@ -407,7 +401,6 @@ See also \figref{bstretch1}, with the force given by: \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 @@ -528,7 +521,6 @@ F_{\mbox{\small FENE}}(\rvij) = \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} @@ -564,7 +556,6 @@ $j$ is in the middle; atoms $i$ and $k$ are at the ends (see \figref{angle}). {\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 @@ -697,7 +688,6 @@ that uses a fourth order polynomial: \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}} @@ -784,7 +774,6 @@ in the {\tt [ dihedraltypes ]} section. 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 @@ -849,7 +838,6 @@ polymer convention (this yields a minus sign for the odd powers of 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} @@ -860,7 +848,6 @@ In {\gromacs} the four term function is implemented: 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.\\ @@ -957,7 +944,6 @@ cases in which $\theta$ and $\phi$ are simultaneously $180^{\circ}$. The integra (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 @@ -997,7 +983,6 @@ $x$ is the dihedral angle in degrees. The table should go from -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 @@ -1125,7 +1110,6 @@ topology. The following potential is used (Figure~\ref{fig:fbposres}B): -%\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 @@ -1177,7 +1161,6 @@ where $\Delta\phi$ is a user defined angle and $k_{dihr}$ is the force 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} @@ -1191,9 +1174,7 @@ refinement}\index{refinement,nmr}. 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. @@ -1240,14 +1221,11 @@ The forces are 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 @@ -1411,13 +1389,11 @@ the column {\tt fac}. The force constant in the parameter file is 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, @@ -1651,9 +1627,7 @@ Some parameters for orientation restraints can be specified in the 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 @@ -1722,9 +1696,7 @@ where $a$ is a magic (dimensionless) constant, usually chosen to be 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} @@ -2001,9 +1973,7 @@ This ``1-1-48'' path is also implemented in {\gromacs}. Note that for this path 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, @@ -2102,7 +2072,6 @@ non-bonded interactions.]{Parameters for the different functional forms of the non-bonded interactions.} \label{tab:funcparm} \end{table} -%} % Brace matches ifthenelse test for gmxlite \newcommand{\vvis}{\ve{r}_s} @@ -2116,7 +2085,7 @@ forms of the non-bonded interactions.} \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) @@ -2371,12 +2340,10 @@ only the mass of the A-state is used for the weight \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}} @@ -2540,7 +2507,6 @@ automates the process of selecting the optimal number of PME-only ranks. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%\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 @@ -2801,7 +2767,6 @@ performance in balancing the load of parallel simulations using 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} diff --git a/docs/manual/gromacs.tex b/docs/manual/gromacs.tex index 9ee87735b8..034d4857f4 100644 --- a/docs/manual/gromacs.tex +++ b/docs/manual/gromacs.tex @@ -1,7 +1,7 @@ % % 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. @@ -69,10 +69,6 @@ pdfinfo={ 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 @@ -97,13 +93,7 @@ pdfinfo={ \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~} @@ -115,28 +105,7 @@ pdfinfo={ \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} @@ -150,7 +119,6 @@ Uppsala University, Sweden. \rhead[\fancyplain{}{\em\leftmark}]{\fancyplain{}{\em\thepage}} \cfoot{} -\ifthenelse{\equal{\gmxlite}{1}}{}{ \begin{center} \phantom{ } \vspace{1cm} @@ -239,7 +207,6 @@ For details, check the COPYING file in the source code or consult 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 @@ -259,13 +226,10 @@ available on our homepage, \wwwpage. Have fun. \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 % @@ -273,7 +237,6 @@ available on our homepage, \wwwpage. Have fun. \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 @@ -297,12 +260,10 @@ available on our homepage, \wwwpage. Have fun. \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} -- 2.11.4.GIT