%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, 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.
them in {\tt atomtypes.atp} as well.
+\section{Molecule definition\index{molecule definition}}
+
+\subsection{Moleculetype entries}
+An organizational structure that usually corresponds to molecules is
+the {\tt [ moleculetype ]} entry. This entry serves two main purposes. One is
+to give structure to the topology file(s), usually corresponding to real
+molecules. This makes the topology easier to read and writing it less labor
+intensive. A second purpose is computational efficiency. The system definition
+that is kept in memory is proportional in size of the {\tt moleculetype}
+definitions. If a molecule is present in 100000 copies, this saves a factor
+of 100000 in memory, which means the system usually fits in cache, which
+can improve performance tremendously. Interactions that correspond to chemical
+bonds, that generate exclusions, can only be defined between atoms within
+a {\tt moleculetype}. It is allowed to have multiple molecules which are
+not covalently bonded in one {\tt moleculetype} definition. Molecules can
+be made infinitely long by connecting to themselves over periodic boundaries.
+When such periodic molecules are present, an option in the {\tt mdp} file
+needs to be set to tell {\gromacs} not to attempt to make molecules
+that are broken over periodic boundaries whole again.
+
+\subsection{Intermolecular interactions\index{intermolecular interaction}}
+In some cases, one would like atoms in different molecules to also interact
+with other interactions than the usual non-bonded interactions. This is often
+the case in binding studies. When the molecules are covalently bound, e.g.
+a ligand binding covalently to a protein, they are effectively one molecule
+and they should be defined in one {\tt [ moleculetype ]} entry. Note that
+{\tt pdb2gmx} has an option to put two or more molecules in one
+{\tt [ moleculetype ]} entry. When molecules are not covalently bound,
+it is much more convenient to use separate {\tt moleculetype} definitions
+and specify the intermolecular interactions in the
+{\tt [ intermolecular\_interactions] } section. In this section, which is
+placed at the end of the topology (see \tabref{topfile1}), normal bonded
+interactions can be specified using global atom indices. The only restrictions
+are that no interactions can be used that generates exclusions and no
+constraints can be used.
\subsection{Intramolecular pair interactions\index{intramolecular pair interaction}}
\label{subsec:pairinteractions}
in separate ``LJ-14'' and ``Coulomb-14'' entries per energy group pair.
Energies for {\tt [~pairs_nb~]} are added to the ``LJ-(SR)'' and ``Coulomb-(SR)'' terms.
-\subsection{Implicit solvation parameters\index{implicit solvation parameters}}
+
+\subsection{Exclusions}
+\label{sec:excl}
+The \normindex{exclusions} for non-bonded interactions are generated by {\tt
+grompp} for neighboring atoms up to a certain number of bonds away, as
+defined in the {\tt [~moleculetype~]} section in the topology file
+(see \ssecref{topfile}). Particles are considered bonded when they are
+connected by ``chemical'' bonds ({\tt [~bonds~]} types 1 to 5, 7 or 8)
+or constraints ({\tt [~constraints~]} type 1).
+Type 5 {\tt [~bonds~]} can be used to create a \normindex{connection}
+between two atoms without creating an interaction.
+There is a \normindex{harmonic interaction}
+({\tt [~bonds~]} type 6) that does not connect the atoms by a chemical bond.
+There is also a second constraint type ({\tt [~constraints~]} type 2)
+that fixes the distance, but does not connect
+the atoms by a chemical bond.
+For a complete list of all these interactions, see \tabref{topfile2}.
+
+Extra exclusions within a molecule can be added manually
+in a {\tt [~exclusions~]} section. Each line should start with one
+atom index, followed by one or more atom indices. All non-bonded
+interactions between the first atom and the other atoms will be excluded.
+
+When all non-bonded interactions within or between groups of atoms need
+to be excluded, is it more convenient and much more efficient to use
+energy monitor group exclusions (see \secref{groupconcept}).
+
+
+\section{Implicit solvation parameters\index{implicit solvation parameters}}
Starting with {\gromacs} 4.5, implicit solvent is supported. A section in the
topology has been introduced to list those parameters:
basis.
-
-\section{Exclusions}
-\label{sec:excl}
-The \normindex{exclusions} for non-bonded interactions are generated by {\tt
-grompp} for neighboring atoms up to a certain number of bonds away, as
-defined in the {\tt [~moleculetype~]} section in the topology file
-(see \ssecref{topfile}). Particles are considered bonded when they are
-connected by ``chemical'' bonds ({\tt [~bonds~]} types 1 to 5, 7 or 8)
-or constraints ({\tt [~constraints~]} type 1).
-Type 5 {\tt [~bonds~]} can be used to create a \normindex{connection}
-between two atoms without creating an interaction.
-There is a \normindex{harmonic interaction}
-({\tt [~bonds~]} type 6) that does not connect the atoms by a chemical bond.
-There is also a second constraint type ({\tt [~constraints~]} type 2)
-that fixes the distance, but does not connect
-the atoms by a chemical bond.
-For a complete list of all these interactions, see \tabref{topfile2}.
-
-Extra exclusions within a molecule can be added manually
-in a {\tt [~exclusions~]} section. Each line should start with one
-atom index, followed by one or more atom indices. All non-bonded
-interactions between the first atom and the other atoms will be excluded.
-
-When all non-bonded interactions within or between groups of atoms need
-to be excluded, is it more convenient and much more efficient to use
-energy monitor group exclusions (see \secref{groupconcept}).
-
\section{Constraint algorithms\index{constraint algorithms}}
\label{sec:constraints}
Constraints are defined in the {\tt [~constraints~]} section.
{\em mandatory} & {\tts molecules} & & & \multicolumn{2}{l|}{molecule name; number of molecules} \\
\dline
\multicolumn{6}{c}{~} \\
+\multicolumn{6}{c}{\bf \large Inter-molecular interactions} \\
+\dline
+{\em optional} & \multicolumn{4}{l}{\tts intermolecular_interactions} & \\
+\hline
+\multicolumn{6}{|c|}{one or more bonded interactions as described in \tabref{topfile2}, with two or more atoms,} \\
+\multicolumn{6}{|c|}{no interactions that generate exclusions, no constraints, use global atom numbers} \\
+\dline
+\multicolumn{6}{c}{~} \\
\multicolumn{6}{l}{`\# at' is the required number of atom type indices for this directive} \\
\multicolumn{6}{l}{`f. tp' is the value used to select this function type} \\
-\multicolumn{6}{l}{`F. E.' indicates which of the parameters for this interaction can be} \\
-\multicolumn{6}{l}{\phantom{`F. E.'} interpolated during free energy calculations} \\
+\multicolumn{6}{l}{`F. E.' indicates which of the parameters can be interpolated in free energy calculations} \\
\multicolumn{6}{l}{~$^{(cr)}$ the combination rule determines the type of LJ parameters, see~\ssecref{nbpar}}\\
\multicolumn{6}{l}{~$^{(*)}$ for {\tts dihedraltypes} one can specify 4 atoms or the inner (outer for improper) 2 atoms}\\
\multicolumn{6}{l}{~$^{(nrexcl)}$ exclude neighbors $n_{ex}$ bonds away for non-bonded interactions}\\
% The footnotetext fields only work inside the body, and not from a
% column with ``p'' formatting'!
bond & {\tts bonds}\fnm{4},\fnm{5} & 2 & 1 & $b_0$ (nm); $k_b$ (\kJmolnm{-2}) & all & \ssecref{harmonicbond}
-\label{tab:topfile2} \footnotetext[1]{The required number of atom indices for this directive}\footnotetext[2]{The index to use to select this function type}\footnotetext[3]{Indicates which of the parameters for this interaction can be interpolated during free energy calculations}\footnotetext[4]{This interaction type will be used by {{\tts grompp}} for generating exclusions}\footnotetext[5]{This interaction type can be converted to constraints by {{\tts grompp}}}\footnotetext[7]{The combination rule determines the type of LJ parameters, see~\ssecref{nbpar}}\footnotetext[6]{No connection, and so no exclusions, are generated for this interaction}
+\label{tab:topfile2} \footnotetext[1]{The required number of atom indices for this directive}\footnotetext[2]{The index to use to select this function type}\footnotetext[3]{Indicates which of the parameters can be interpolated in free energy calculations}\footnotetext[4]{This interaction type will be used by {{\tts grompp}} for generating exclusions}\footnotetext[5]{This interaction type can be converted to constraints by {{\tts grompp}}}\footnotetext[7]{The combination rule determines the type of LJ parameters, see~\ssecref{nbpar}}\footnotetext[6]{No connection, and so no exclusions, are generated for this interaction}
\\
G96 bond & {\tts bonds}\fnm{4},\fnm{5} & 2 & 2 & $b_0$ (nm); $k_b$ (\kJmolnm{-4}) & all & \ssecref{G96bond} \\
Morse & {\tts bonds}\fnm{4},\fnm{5} & 2 & 3 & $b_0$ (nm); $D$ (\kJmol); $\beta$ (nm$^{-1}$) & all & \ssecref{Morsebond} \\
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff