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.
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