[gmx-developers] charge groups

[Gerrit Groenhof]

> 
> Hello developer fellows,
> 
> Can somebody tell me where the charge group indices are stored (the 
> variable names, eventually the structure name and include file). I did 
> some fishing by myself but no luck so far :-( They are used to check for 
> the consistency definition of energy monitor groups.
> 
> Thanks,
> 
> Valentin

Hi  Valentin

It might be handy to have a look at my gromacs sheets
(http://md.chem.rug.nl/~groenhof/blocks.html) while reading this.....

In topology.h the topology is defined and one part of it is the
charges groups:

top struct: (include/types/topology.h)

..
blocks[ebNR] (ebNR is the number of diffent blocks used in gmx)
..

number ebCGS (see gmxlib/names.c) of this block array is the
chargegroup block.

Charge groups is a block (block.h).

block struct: (include/types/block.h)
nr
index[]
nra
a[] 

So charge group i contains the atoms a[index[i]] until
a[index[i+1]]. The elements of a[] are the atomnumbers of these
atoms. 


I hope I helped you a bit in the right direction,

groetjes,

Gerrit