[gmx-users] using atom id to specify the position_restraints
feenstra at few.vu.nl
Mon Feb 7 17:57:48 CET 2005
David van der Spoel wrote:
> On Sun, 2005-02-06 at 17:15 +0000, Binbin Liu wrote:
>>I have two questions.
>>1. Is it possible to partially freeze pariticular ions during the energy
>>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.
If you need restrained and unrestrained ions of the same type (e.g.
Na+), you will have to make two [moleculetype] sections (for Na+), one
with position restraints on atom 1 (say, NaR), and one without (Na+).
Then the system section in your .top should read something like:
Ions in water
Which would make the first 15 Na's in your .gro file position restraint.
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