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

[BON Michael]

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.

Thanks for your help,

Michael Bon
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