[gmx-developers] iparams size question

[David van der Spoel]

On 2013-04-06 20:19, Mark Abraham wrote:
>
>
> On Sat, Apr 6, 2013 at 7:52 PM, francesco oteri
> <francesco.oteri at gmail.com <mailto:francesco.oteri at gmail.com>> wrote:
>
>     Dear gromacs developers,
>     on the webpage describing the data sructures
>     (http://www.gromacs.org/Developer_Zone/Programming_Guide/Data_Structures)
>     it is written that "t_iparams *iparams; ///matrix of size atnr² with
>     interaction params"/
>
>     but looking at the different part of the code (ex pr_iparams in
>     txtdump.c) it is clear that in iparams there are all the parameters
>     for the possible nteractions, so for sure is more than atnr**2 and
>     it seems to me that the size should be ntypes.
>
>     Am I wrong?
>
>
> Probably not. The code is definitive. The size of a matrix is whatever
> it was given when it was allocated. A comment is a doubtful secondary
> source of information. A webpage is even less likely to be definitive :-)
>
> That programming guide was contributed by a user some years ago, and
> AFAIK could have any sort of inaccuracies. One of the lessons of history
> is that documentation that is not in the code does not get maintained
> when the code changes. For 5.0, there are plans to a) document better,
> and b) make that available via Doxygen.

The comment applies to the matrix of non-bonded parameters (LJ or 
Buckingham) which is the square of the number of atomtypes. On top of 
that there are the bonded interactions.
>
> Mark
>
>
>     Francesco
>
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>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se