[gmx-developers] iparams size question
francesco.oteri at gmail.com
Sun Apr 7 11:20:19 CEST 2013
So, in iparams there are non-bonded parameters + bonded,
that is (atnr² + bonded) number of entryes, am I right?
2013/4/7 David van der Spoel <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<francesco.oteri at gmail.com>>>
>> Dear gromacs developers,
>> on the webpage describing the data sructures
>> 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.
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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
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Cordiali saluti, Dr.Oteri Francesco
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