[gmx-users] Atom index (13154) in position_restraints out of bounds

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 11 14:33:45 CET 2012

No. Bonded interactions (such as distance restraints) can only be defined
between atoms present in the same [moleculetype]. OTOH a [moleculetype]
doesn't care whether any bonded interactions exist between its atoms or
not, so as long as you obey the constraint that the atom ordering implied
by your [molecules] ordering and ordering of [atoms] within [moleculetypes]
must match that of the coordinate file given to grompp, you're fine. Atom
numbering in the coordinate file to grompp is not important (but you get
told if there's mismatches, IIRC).


On Tue, Dec 11, 2012 at 7:23 AM, Yun Shi <yunshi09 at gmail.com> wrote:

> Hi all,
> I want to restrain the OW of a bound water molecule for the MD of a
> protein in water. But the index of this OW is apparently out of range
> and I know someone would suggest merging this water with my protein
> (e.g. put them in the same .itp file) so as to make them "one
> molecule" and thus the index would not be out of bounds.
> But I wonder if there is any other way to circumvent this issue?
> Thanks,
> Yun
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