Added reference to cmap in pdb2gmx.

Fixes #886.

Change-Id: Ib4c84a50962ed90ce145ad001322a9a46c8a2ab0

diff --git a/manual/forcefield.tex b/manual/forcefield.tex
index 1d35f33116a6a73e597ab59bcc61cf60e2ad38f0..9ffa55cc044a3b8c2d57b85424ffb9dc2aecf0f7 100644 (file)
--- a/manual/forcefield.tex
+++ b/manual/forcefield.tex
@@ -2898,6 +2898,7 @@ As of version 4.5, {\gromacs} provides native support for the following AMBER fo
 \end{itemize}
 
 \subsection{CHARMM\index{CHARMM force field}}
 \end{itemize}
 
 \subsection{CHARMM\index{CHARMM force field}}

+\label{subsec:charmmff}

 
 As of version 4.5, {\gromacs} supports the CHARMM27 force field for proteins~\cite{mackerell04, mackerell98}, lipids~\cite{feller00} and nucleic acids~\cite{foloppe00}. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested -- both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with {\gromacs}-specific techniques such as virtual sites (enabling long time steps) and a fast implicit solvent recently implemented~\cite{Larsson10} -- and the details and results are presented in the paper by Bjelkmar et al.~\cite{Bjelkmar10}. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
 
 
 As of version 4.5, {\gromacs} supports the CHARMM27 force field for proteins~\cite{mackerell04, mackerell98}, lipids~\cite{feller00} and nucleic acids~\cite{foloppe00}. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested -- both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with {\gromacs}-specific techniques such as virtual sites (enabling long time steps) and a fast implicit solvent recently implemented~\cite{Larsson10} -- and the details and results are presented in the paper by Bjelkmar et al.~\cite{Bjelkmar10}. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
 

diff --git a/manual/topology.tex b/manual/topology.tex
index c6f6fddc38676ce73e3925079f8cc140aff8d8c0..c5638116b5e48593c39062e7d4d3954b18dcacf2 100644 (file)
--- a/manual/topology.tex
+++ b/manual/topology.tex
@@ -737,7 +737,9 @@ number of all angles needs to be specified.
 bond, preferably on heavy atoms. When the {\tt [~dihedrals~]} field is used,
 no other dihedrals will be generated for the bonds corresponding to the
 specified  dihedrals. It is possible to put more than one dihedral
 bond, preferably on heavy atoms. When the {\tt [~dihedrals~]} field is used,
 no other dihedrals will be generated for the bonds corresponding to the
 specified  dihedrals. It is possible to put more than one dihedral

-function on a rotatable bond. 
+function on a rotatable bond. In the case of CHARMM27 FF {\tt pdb2gmx}
+can add correction maps to the dihedrals using the default {\tt -cmap} option.
+Please refer to \ssecref{charmmff} for more information.

 
 {\tt pdb2gmx} sets the number of exclusions to 3, which
 means that interactions between atoms connected by at most 3 bonds are
 
 {\tt pdb2gmx} sets the number of exclusions to 3, which
 means that interactions between atoms connected by at most 3 bonds are