[gmx-users] double sids error ? what ?!

[David van der Spoel]

BON Michael wrote:
> 
> Hi all,
> 
> I got a "double sids error" when using grompp. What does it mean in the first place ?
> 
> Apparently, it has to do with Lincs making shake-blocks when using constraint = all-bonds.
> I am simulating two strands of RNA, defined in the same .top file as I want to add some distance restraint 
> between the two strands. I add some dummy atoms on a strand, and the problem occurs when I define bonds (type 1)
> linking those dummy atoms to the second one (maybe the fact that it is the second strand is coincidental). The problem disappear when I define a bond type 6 instead, or when I use constraint=all-bonds.
> I may have done some mistakes in the definition of my topology, but I can't poin them because I don't understand what a double sids error is.
> 

sid = shake id

it means one atom is in multiple shake blocks
it should not happen, but hey, sometimes life is unfair.
Anyway, I think bond type 6 is what you need to use in these kind of cases.

> Thanks for your help,
> 
> Michael Bon
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se