From: Rossen Apostolov Date: Tue, 17 Jun 2014 12:16:50 +0000 (+0200) Subject: Added reference to cmap in pdb2gmx. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=43244544d12d94a8569d167479d14c8d8ac8cd01;p=alexxy%2Fgromacs.git Added reference to cmap in pdb2gmx. Fixes #886. Change-Id: Ib4c84a50962ed90ce145ad001322a9a46c8a2ab0 --- diff --git a/manual/forcefield.tex b/manual/forcefield.tex index 1d35f33116..9ffa55cc04 100644 --- 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}} +\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. diff --git a/manual/topology.tex b/manual/topology.tex index c6f6fddc38..c5638116b5 100644 --- 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 -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