[gmx-users] manual inconsistency

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 1 05:52:15 CET 2006


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 

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?



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