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

[Justin Lemkul]

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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================