[gmx-users] manual inconsistency

David Mobley dmobley at gmail.com
Wed Feb 1 16:54:48 CET 2006


Is the 3.3 manual out yet? I still don't see it anywhere; I thought it
was being released with 3.3.1.


On 1/31/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Hi,
> 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?
> Regards,
> Mark
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