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

[Anton Feenstra]

David van der Spoel wrote:

> 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.

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:
[system]
  Ions in water
[molecules]
SOL	51467
NaR	   15
Na+        25
Cl-        40

Which would make the first 15 Na's in your .gro file position restraint.

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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