[gmx-developers] curious about t_mdatoms

David spoel at xray.bmc.uu.se
Fri Jul 5 14:51:33 CEST 2002

On Fri, 2002-07-05 at 13:05, Vishal Vaidyanathan wrote:
> Hi,
>   Can somebody explain very briefly why we have a t_mdatoms structure? I
> mean why take all the trouble of md2atoms() and atoms2md()? I guess it has
> something to do with optimizing for speed, but a quick explanation would
> help!
>   This is not important for my current coding anyway, but I was just
> curious. :-)
You're right it is messy. It is indeed to have simple linear arrays for
in particular charges and types. These are the only thing that go into
the innerloops. The energy group index is used in neighboursearching,
some of the other group indices in the update bit.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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