[gmx-users] using atom id to specify the position_restraints

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 6 09:32:38 CET 2005

On Sun, 2005-02-06 at 17:15 +0000, Binbin Liu wrote:
> Dear all,
> I have two questions.
> 1. Is it possible to partially freeze pariticular ions during the energy 
> minimisation?
> 2. Persumbly the answer to question 1 is yes. I use position_restraints in 
> .top to freeze ions. Grompp gives warning:
> fatal error: Atom index (69338) in position_restraints out of bounds (1-1)
You should edit the ions.itp file and put the position restraint in
there. The number in the position restraint is the index in the molecule
type, for an ion you can there for only select 1.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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