[gmx-users] manual inconsistency

Berk Hess gmx3 at hotmail.com
Wed Feb 1 17:46:23 CET 2006

>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Gromacs Users <gmx-users at gromacs.org>
>Subject: [gmx-users] manual inconsistency
>Date: Wed, 01 Feb 2006 15:52:15 +1100
>In section 5.6.1 of the gromacs 3.3 manual (which deals with the 
>description of the format of the .top topology file), table 5.3 implies 
>that the lines following the dihedraltypes directive must have the form of 
>two atom types, followed by the function type, followed by the parameters.
>In fact, as made clear in kernel/toppush.c, lines with four atom types, 
>function type and parameters are also read.
>What is the behaviour of gromacs when dealing with such four atom-type 
>dihedrals? Does it implement them correctly by matching all four atoms, or 
>does it drop the extra information and only match dihedraltypes on the 
>central two atoms? Can the manual please be updated to reflect whichever of 
>these is true?

It matches all four atoms (otherwise there would have also been
no point in implementing this feature).

The person who implemented this should add it to the manual.


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