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

Justin Lemkul jalemkul at vt.edu
Tue Dec 11 14:32:16 CET 2012

On 12/11/12 1:23 AM, Yun Shi 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?

Position restraints can only be applied per [moleculetype] block, so the global 
numbering cannot be used.  The water molecule you wish to restrain must be 
either (1) in its own block or (2) within another, i.e. the protein.



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


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