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.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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