[gmx-developers] iparams size question

[David van der Spoel]

On 2013-04-07 11:20, francesco oteri wrote:
> So, in iparams there are non-bonded parameters + bonded,
> that is (atnr² + bonded) number of entryes, am I right?
>
yes.

> Francesco
>
> 2013/4/7 David van der Spoel <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>
>
>     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>
>         <mailto: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
>         <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
>     <tel:%2B46184714205>.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
>


-- 
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