[gmx-users] cgnr order

[David van der Spoel]

Stephanie Bluebear wrote:
> Dear Simulators,
> 
> Do the numbers in the cgnr column necessarily need to be in ascending 
> order? I have a topology of a molecule and would like to acetylate some 
> residues, whose atoms numbers (and charge group numbers) are in the 
> middle of the pack . I have added the atoms I need to add at the end of 
> the [atoms] directive. The new charge groups include some of the new and 
> old atoms, to ensure integer charge values.  However, this means the 
> cgnrs are not ascending any more. Is this allowed?

No. Atom 302 will be put in its own charge group.
As long as you use PME this is not a problem though. When you use Cutoff 
or RF it will generate artifacts.
> 
> e.g.
> 
> [atoms]
> nr ................cgnr     charge
> 1   ................ 1               0.3333          
> 2    ................1              -0.6666
> 3    ................2               0.0000
> 4    ................3               0.5000  
> .........................
> .........................
> 302 ..............1              0.333333
> 
> 
> Thanks in advance.
> 
> Stephanie
> 
> 
> 
> 
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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