[gmx-users] Grompp failed under double precision

Justin A. Lemkul jalemkul at vt.edu
Mon Dec 7 01:43:54 CET 2009

Jack Shultz wrote:
> We have a workflow going, and I switched to double precision because
> of the LINCS issues. I got this error now with grompp. I don't think
> anything else is different other than double precision, but I included
> the logs for this.
> -------------------------------------------------------
> Program grompp_d, VERSION 4.0.5
> Source code file: toppush.c, line: 1273
> Fatal error:
> [ file spce.itp, line 32 ]:
> Atom index (1) in bonds out of bounds (1-0).
> This probably means that you have inserted topology section "bonds"
> in a part belonging to a different molecule than you intended to.
> In that case move the "bonds" section to the right molecule.
> -------------------------------------------------------

Please see the following:


Particularly of interest is the section within about the AMBER force fields, for 
which the default spc.itp is incompatible.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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