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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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